Transcriptome wiring analysis in parkinson&#39;s disease and uses thereof

ABSTRACT

The invention is directed to methods to identify predisposition or risk to develop Parkinson&#39;s disease, methods to identify agents which have therapeutic effect on Parkinson&#39;s disease, and methods to determine the therapeutic effect of an agent in a subject suffering from Parkinson&#39;s disease, and to kits and reagents for carrying out the methods of the invention.

This application claims the priority to Application Ser. No. 61/566,925 filed Dec. 5, 2011, the content of which is hereby incorporated in its entirety.

This invention was made with government support under RO1NS064433 awarded by NIH-NINDS. The government has certain rights in the invention.

The contents of all patents, patent applications and non-patent references listed in the specification are incorporated by reference herewith.

BACKGROUND

Parkinson's disease (PD) is a degenerative disorder of the central nervous system. It results from the death of dopamine-containing cells in the substantia nigra, a region of the midbrain; the cause of cell-death is unknown. Early in the course of the disease, the most obvious symptoms are movement-related, including shaking, rigidity, slowness of movement and difficulty with walking and gait. Later, cognitive and behavioral problems may arise, with dementia commonly occurring in the advanced stages of the disease. Other symptoms include sensory, sleep and emotional problems. PD is more common in the elderly with most cases occurring after the age of 50.

Parkinson's disease is diagnosed by a physician exam, and diagnosis is based on the medical history and a neurological examination of the patient. There is no laboratory or molecular test that will clearly identify the disease. Brain scans are sometimes used to rule out disorders that could give rise to similar symptoms. Patients may be given levodopa, or other dopamine affecting agent, and resulting relief of motor impairment tends to confirm diagnosis. The finding of Lewy bodies in the midbrain on autopsy is usually considered proof that the patient suffered from Parkinson's disease. Thus there is need for biomarkers for PD disease or treatment.

SUMMARY

In certain aspects, the invention provides methods to determine predisposition or risk to develop Parkinson's Disease (PD) in a subject in need thereof comprising: (a) providing a biological sample from a subject in need thereof, (b) determining a ratio of SNCA long transcript to SNCA total transcript in the subject's biological sample and (c) comparing the ratio of SNCA long transcript to SNCA total transcript from the subject sample to a reference ratio of SNCA long transcript to SNCA total transcript, wherein the reference ratio is associated with a non-PD status, and wherein an increased ratio of SNCA long transcript to SNCA total transcript in the subject's sample compared to the reference ratio of SNCA long transcript to SNCA total transcript is indicative of a risk for developing Parkinson's Disease.

In certain aspects, the invention provides methods to diagnose PD in a subject in need thereof, the method comprising: (a) providing a biological sample from a subject in need thereof, (b) determining a ratio of SNCA long transcript to SNCA total transcript in the subject's sample and (c) comparing the ratio of SNCA long transcript to SNCA total transcript from the subject's sample to a ratio of SNCA long transcript to SNCA total transcript in a reference sample from healthy individuals/non-PD status, wherein an increased ratio of SNCA long transcript to SNCA total transcript in the subject's sample compared to the ratio of SNCA long transcript to SNCA total transcript in the reference non-PD status sample indicates that the subject is suffering from Parkinson's Disease.

In certain embodiments, the methods further comprise comparing the ratio of SNCA long transcript to SNCA total transcript from the subject to a reference ratio of SNCA long transcript to SNCA total transcript for a PD disease status; wherein a ratio of SNCA long transcript to SNCA total transcript in the subject's sample which is similar or comparable to the reference ratio of SNCA long transcript to SNCA total transcript for a PD status indicates that the subject is suffering from PD.

In certain aspects, the invention provides methods to diagnose PD in a subject in need thereof, comprising: (a) providing a biological sample from a subject, (b) determining a ratio of SNCA long transcript to SNCA total transcript in the sample obtained from the subject; (c) comparing the ratio of SNCA long transcript to SNCA total transcript from the subject to a reference ratio of SNCA long transcript to SNCA total transcript for a PD disease status; wherein a ratio of SNCA long transcript to SNCA total transcript in the subject's sample which is similar or comparable to the reference ratio of SNCA long transcript to SNCA total transcript for a PD status indicates that the subject is suffering from PD.

In certain embodiments, the methods further comprise comparing the ratio of SNCA long transcript to SNCA total transcript from the subject's sample to a ratio of SNCA long transcript to SNCA total transcript in a reference sample from healthy individuals/non-PD status, wherein an increased ratio of SNCA long transcript to SNCA total transcript in the subject's sample compared to the ratio of SNCA long transcript to SNCA total transcript in the reference non-PD status sample indicates that the subject is suffering from Parkinson's Disease.

In certain embodiments, the PD disease status is determined by any suitable method, including but not limited to a physical examination of the subject, a neurological examination of the subject, a brain scan, or a combination thereof. In certain embodiments, the subject is not diagnosed with PD.

In certain embodiments, the methods further comprise a physical examination of the subject, a neurological examination of the subject, a brain scan, or a combination thereof.

In certain embodiments, the methods further comprise a step of sequencing nucleic acids isolated from the subject's sample to determine the presence or absence of a PD-risk associated SNP, wherein the presence of a PD-risk associated SNP is further indicative that the subject is at risk of developing PD or is suffering from PD. In certain embodiments, the SNP is rs356168C/C risk-associated variant, rs356165 risk-associated variant, rs2736990 risk-associated variant, any other risk associated SNP, or any combination thereof, or any other suitable SNP.

In certain embodiments, the subject is suspected of having PD or is at risk of developing PD based on the presence of any one of parkinsonism symptoms, determined by any suitable method, including but not limited to a physical examination of the subject, a neurological examination of the subject, a brain scan, or a combination thereof.

In certain embodiments, the methods are carried out in the absence or presence of dopamine affecting agent administered to the subject, wherein an increased ratio of SNCA long transcript to SNCA total transcript in the presence of dopamine compared to the ratio of SNCA long transcript to SNCA total transcript in the absence of dopamine is indicative of a subject having an increased risk to develop PD.

In certain aspects, the invention provides methods to identify a candidate agent which has a therapeutic effect on PD, the method comprising: (a) providing a sample from a cortical neuron cell culture, (b) determining a ratio of SNCA long transcript to SNCA total transcript in a sample from the cortical neuron cell culture, wherein the sample is obtained in the presence and absence of a candidate agent, wherein a lowered ratio of SNCA long transcript to SNCA total transcript in the sample in the presence of the candidate agent is indicative of an agent which is a therapeutic agent for treatment of PD.

In certain aspects, the invention provides methods to identify a candidate agent which has a therapeutic effect on PD, the method comprising: (a) providing a sample from an animal model of PD; (b) determining a ratio of SNCA long transcript to SNCA total transcript in the sample from an animal model of PD, wherein the sample is obtained in the presence and absence of a candidate agent, administered to the animal model of PD, wherein a lowered ratio of SNCA long transcript to SNCA total transcript in the sample in the presence of the candidate agent is indicative of an agent which is a therapeutic agent for treatment of PD.

In certain aspects, the invention provides methods to determine a therapeutic effect of a candidate agent in a subject suffering from PD, the method comprising: (a) determining a ratio of SNCA long transcript to SNCA total transcript in a sample from a subject suffering from PD, wherein the sample is obtained in the presence and absence of a candidate agent, wherein a lowered ratio of SNCA long transcript to SNCA total transcript in the sample in the presence of the candidate agent is indicative of an agent which is a therapeutic agent for treatment of PD.

In certain embodiments of the methods, the lowered ratio of SNCA long transcript to SNCA total transcript in the sample in the presence of the candidate agent is due to a reduced level of SNCA long transcript in the presence of the candidate agent compared to level of SNCA long transcript the absence of the candidate agent.

In certain embodiments of the methods, the subject is diagnosed with PD and is not administered dopamine affecting agents (i.e. not treated for PD).

In certain embodiments of the methods, the subject is diagnosed by clinical symptoms, imaging of dopamine uptake, or combination thereof.

In certain embodiments of the methods, a ratio of SNCA long transcript to SNCA total transcript is determined by quantifying SNCA long transcript and SNCA total transcript.

In certain embodiments, the methods further comprise isolating nucleic acids from the subject's biological sample.

In certain embodiments, the methods further comprise quantifying the levels of SNCA long transcript and SNCA total transcript, wherein the levels of SNCA long transcript and SNCA total transcript are quantified by RT-qPCR, or any other suitable method.

In certain embodiments, the ratio of SNCA long transcript to SNCA total transcript is determined in a CSF sample, blood sample, plasma, or serum.

The invention provides a kit comprising PCR primers to carry out step (b) of the method of any one of the methods and instructions to carry out steps (a), (b) and (c) of these methods.

A kit comprising at least one PCR primer to selectively quantify the SNCA long transcript and SNCA total transcript in a sample from a subject according to any one of the methods, so as to determine the ratio of SNCA long transcript and SNCA total transcript, and instructions to carry out steps (a) and (b) of the method of any of the methods.

The present invention is based on the discovery that there is an increase in the SNCA long transcript to SNCA total transcript ratio in a PD patients relative to individuals unaffected by PD. The invention provides use of ratio of SNCA long transcript to SNCA total transcript in a subject's sample as a biomarker of PD disease or treatment. The invention provides use of ratio of SNCA long transcript to SNCA total transcript in a subject's sample to diagnose PD, or to confirm diagnosis of PD established by other criteria, or to determine predisposition or risk of a subject to develop PD.

Determining predisposition or risk of a subject to develop PD, or diagnosis of PD is done by comparing the ratio of SNCA long transcript to SNCA total transcript from a subject's sample to a ratio of SNCA long transcript to SNCA total transcript from a control sample, wherein an increased ratio of SNCA long transcript to SNCA total transcript in the subject's sample compared to the ratio of SNCA long transcript to SNCA total transcript in the control sample is indicative of a subject who has developed PD or of a subject who has increased risk for developing Parkinson's Disease. In certain embodiments of the methods optionally include review of medical history, conducting neurological examination, conducting brain scans to exclude PD-like symptoms, administering of dopamine affecting agents to determine if there is an improvement in the parkinsonism symptoms, for example but not limited to levodopa, or any other dopamine affecting agent.

In the instant methods, the subject's sample is a biological sample, including but not limited to a blood sample, plasma sample, serum, CSF, tissue, cell or any combination thereof. Methods to isolate nucleic acid sequences from biological samples are known in the art. Methods for quantitative determination of amount of nucleic acids in a biological sample are known in the art.

Common genetic variants in the human population may play a significant role in the pathogenesis of Parkinson's disease (PD) and other neurodegenerative disorders. As the majority of identified PD-associated variants do not alter protein coding, it is presumed that they modify gene expression, although direct evidence for this has been limited. Included herein are the results of a global transcriptome differential wiring analysis of PD patient and unaffected control brain tissues which identify a unique transcript isoform of aSynuclein (aSyn) with an extended 3′UTR, aSynL, that exhibits a dramatic correlation pattern change in diseased tissue. Strikingly, aSynL is even dyswired from other aSyn transcripts with shorter 3′UTRs, suggesting a pathogenic role for altered aSyn 3′UTR usage in disease. Consistent with this, a genome-wide association study identifies disease-associated polymorphisms within the aSyn and Parkin loci as key genetic factors in aSyn 3′UTR selection. An additional determinant of aSyn 3′UTR selection is intracellular dopamine content, suggesting a mechanism for the propensity of dopaminergic neuron cell loss in PD patient brain. Finally, we show that differential 3′UTR usage modifies the accumulation and localization of aSyn protein. Taken together, these findings identify a unifying mechanism for PD pathogenesis in the context of genetic and environmental variation.

In certain aspects the invention provides that the wiring effect on aSynL with respect to aSyn short is seen in unaffected people with disease-associated SNPs at the aSyn 3′UTR region. This effect cannot possibly be a secondary effect of the disease, as these people are unaffected.

In other aspects, the invention provides that with respect to the aSynL:total ratio, evidence for causality is that, genome wide in unaffected individuals, the top SNP that modifies the aSyn ratio is at the aSyn 3′UTR. Clearly, the SNP effect is causal, as the SNP is a genomic element.

In other aspects the invention provides the effect of the aSynL 3′UTR and SNPs on protein and localization, increase translation and mitochondrial localization.

In other aspects the invention provides that in unaffected human cortical brain samples an increase mitochondrial accumulation of aSyn protein corresponding to the PD-associated allele of the SNCA locus, thus bridging the different findings.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. Altered aSyn transcript co-expression networks in PD brain tissue. a-c, aSyn transcripts are globally rewired in PD brain tissue. a, the normalized DW score (y-axis) is plotted against the DE (x-axis, plotted in log2) between PD and unaffected control brain tissue cohorts. Each circle represents the DW and DE values for an Affymetrix probeset specific for an annotated transcript. The aSyn probeset GDW, 204467_s_at, highlighted in red, is most differentially wired in meta-analysis across all datasets, but is not among the most differentially expressed. b, Schematic representation of aSynL network rewiring in PD. aSyn transcripts recognized by the aSyn 204467_s_at probeset (aSynL) are shown in green. c, Correlation tables for the aSynL-specific 204467_s_at probeset in unaffected control (left) and in PD brain tissue (right) cohorts. High correlations (r=1) are denoted in red, high anti-correlation (r=−1) in blue and weak correlation in white (r=0); see methods for details. aSyn Probeset 204467_s_at is highlighted in green; a second aSyn probeset, 211546_x_at, is highlighted in blue. n=10 for unaffected, n=15 for PD. d-g, A loss of correlation in expression levels of aSyn transcript isoforms is specifically associated with PD. d, Schematic map of microarray probesets targeting aSyn mRNA CDS (blue shades) or 3′UTR (green shades). e, Correlation tables of aSyn isoform expression, as quantified by indicated probesets, in PD SN tissue samples (or unaffected controls; left panels, n=15 and 10 per group) and in an independent cohort of laser-microdissected SN dopamine neurons from PD patient tissue (or unaffected controls, as indicated; right panels; n=10 and 18 per group). High correlation (r=1) is depicted in red, weak correlation (r=0) in yellow. aSynL transcripts are relatively unwired from shorter transcripts in the PD samples. f, In contrast to PD SN patient tissue, aSyn transcript co-expression correlation is not modified in other neuropathology, such as cortical tissue from patients with sporadic FTLD-U or FTLD-U with Progranulin mutations (GSE13162, n=56). g, aSyn transcript co-expression was quantified in cortical tissue from 183 unaffected control individuals (GEO GSE15222) grouped according to their genotype for the PD-associated SNP PD risk-associated. Individuals harbor either 0 PD-risk allele (“CC”, left), 1 PD-risk allele (“CT”, middle) or 2 (“TT”, right). The homozygous disease-associated rs356168 CC genotype is associated with decreased correlation.

FIG. 2. Characterization of aSyn mRNA 3′UTR isoforms in unaffected and PD brain tissue. a, Mapping of pA-RNAseq reads from cerebral cortex brain samples of an unaffected individual (upper panel) and a PD patient (lower panel). The region shown encompasses the vicinity of the aSyn 3′UTR (chr4: 90,645,134-90,647,870 of human genome build hg19). Each blue rectangle represents an individual read at the 3′ end of a polyA transcript (middle panel). The most common aSyn 3′UTR species identified by pA-RNAseq analysis are schematized in the lower panel, grouped as short (in shades of green; 290, 480 or 560 nt), medium (in orange; 1070 nt) or long (red; 2520 nt) species. b, Relative abundance of the different aSyn 3′UTR species, as determined by pA-RNAseq analysis of 17 cortical brain samples from unaffected individuals. The frequency of each 3′UTR species color coded as in a) is expressed as the percentage of total aSyn transcript, averaged across the 17 individuals. Error bars are SEM. c, Northern blot analysis of RNA from human total brain reference or SH-SY5Y cells, as indicated. Blots were hybridized with probes targeting the aSyn CDS (Left panel; relative probe position shown below the dashed line in b, as dark blue bar) and the 3′UTR (Right panel; position shown in b as light blue bar). Nucleotide length is presented on the right; the corresponding 3′UTR size (color coded as per a) is indicated on left. d, Ratio of long 3′UTR aSyn mRNA to short 3′UTR aSyn mRNA species counts, evaluated by pA-RNAseq of cortical samples from unaffected individuals (n=17, black diamonds) and from PD patients (n=17, red triangles). Errors bars are SEM; *:p<0.05, two-tailed t-test, e, Ratio of aSynL:total transcript ratio, as quantified by RT-qPCR in cortical samples from PD (n=18), ALS (n=16) and unaffected individuals (n=8). Error bars are SEM; *:p<0.05, ANOVA followed by post-hoc Bonferroni multiple comparison test. f, aSynL:total aSyn transcript ratio in cortical tissue from 188 unaffected control individuals grouped according to their genotype for the PD-associated SNP PD risk-associated. Individuals harbor either 0 PD-risk allele (“CC”, left), 1 PD-risk allele (“CT”, middle) or 2 (“TT”, right). The statistical significance of the association between the allelic load of the variant and the ratio, as presented, was evaluated by GPLINK assoc function for quantitative traits (see Methods).

FIG. 3. Genome-wide association study for genetic determinants of aSyn transcript isoform ratio. a-b, Manhattan plot representing the SNPs associated with aSynL:total ratio. Association was evaluated for 380,157 SNPs in 364 cortical brain samples for quantitative traits association (see Methods for details). X-axis represents chromosomal location, Y-axis represents −log10 of the unadjusted p-value of association of each SNP with elevated aSyn transcript ratio. The aSyn 3′ locus SNP rs356168 (arrow) exhibited the highest association. SNPs above the p=10e-3 low-stringency threshold (blue line) were selected for further evaluation by Venn diagram analysis in (b; blue circle), and overlapping loci (within 75 kb of a given SNP) that are additionally associated with PD risk ⁹ are presented. c, Loci associated with both PD risk and aSynL:total ratio are presented (combination p-values are quantified as the geometric product of the individual p-values). d, aSynL:total ratio, quantified by RT-qPCR in whole brains of Parkin KO mice (n=4) or control mice (n=5). Error bars are SEM; **:p<0.01:two-tailed t-test.

FIG. 4. Dopaminergic and GABAergic modulation of the aSyn transcript isoform ratio. a, Rat primary cortical cultures were exposed to extracellular dopamine (0, 10, or 100 μM as indicated) and subsequently the aSynL:total ratio was quantified by RT-qPCR. High extracellular dopamine (100 μM) significantly increased the transcript ratio. b, I-Dopa treatment (20 mg/kg intraperitoneal injection daily for 5 days) of 2 month-old control (DAT-Cre/Dicer^(flox/+)) mice but not Dicer—deficient mice (DAT-Cre/Dicer^(flox/flox)); which have lost >95% of mDNs²⁴) led to a significantly increased aSynL:total ratio in midbrain tissue, as quantified by RT-qPCR. c, SHSY-5Y cells were cultured for 8 h in the presence of EU (to label newly transcribed RNA; ‘pulse’) and subsequently cultured in the absence of EU for the indicated period of time (0 h, 8 h, or 16 h; ‘chase’). EU-labeled nascent RNA, as well as total RNA, were then isolated from cell lysates and analyzed by RT-qPCR to evaluate the aSynL:total ratio. Pulse-chase analyses were conducted in the absence of dopamine (‘vehicle’; blue line in upper graph), in the presence of 100 μM dopamine during the EU labeling period only (‘dopamine pulse’; red line in graph and schematic), or during the chase exclusively (‘dopamine chase’; yellow line in graph and schematic). n=5 per group, errors bars are SEM. d, Primary cortical neuron cultures derived from aSyn PAC transgenic mice at day 4 in vitro (DIV) were treated with dopamine (100 μM), picrotoxin (100 μM), or vehicle for 24 h, and then subjected to in situ hybridization (ISH) with probes for human aSyn CDS (red) or specific for aSyn long 3′UTR (blue). Cells were co-stained with antibodies to aSyn (green) and observed by confocal microscopy. The subcellular localization of the different RNA species did not appear distinct. e, Ratio of In situ hybridization signals from probes as in d. Signal was quantified as particle count per neuron. n>10 neurons/group from 3 independent wells; error bars are SEM; ***:p<0.001, ANOVA followed by Bonferroni post hoc test versus the corresponding vehicle treatment. f, Schematic representation of the action of DAT and VMAT2 in dopaminergic neurons. DAT facilitates intracellular uptake of dopamine and thus sensitizes these cells to extracellular dopamine VMAT2 expression enables sequestration of dopamine into vesicles and away from other cytoplasmic constituents, and is thus protective. g, Rat primary cortical cultures were resistant to low extracellular dopamine (10 μM for 24 h; in the absence of DAT overexpression), whereas transfection of a vector encoding DAT sensitized these cells to extracellular dopamine (10 μM for 24 hrs), leading to an increased aSynL:total ratio as quantified by RT-qPCR.

FIG. 5. Regulation of aSyn translation through 3′UTR cis-acting elements. a, SH-SY5Y cells were treated with dopamine (100 μM), picrotoxin (100 μM) or vehicle for 48 h. Total endogenous aSyn protein levels were measured by ELISA and normalized to the total protein levels as assesses by BCA assay, n=5/group, *:p<0.05,**:p<0.01, ANOVA followed by Bonferroni post hoc test versus corresponding vehicle-treatment. b, I-Dopa treatment (20 mg/kg intraperitoneal injection daily for 5 days) of 2 month-old aSyn transgenic PAC mice led to a significantly increased aSyn protein in midbrain tissue, as quantified by ELISA, normalized to total protein level as measure by BCA. n>5 mice/group; *:p<0.05, ANOVA followed by Bonferroni post-hoc test versus corresponding vehicle-treated for each region. c, Schematic map of the aSyn 3′UTR displays the localization of known SNPs with the frequency of their minor alleles >1% in HapMap Caucasian panels. d, Human SHSY-5Y cells were transfected with a firefly luciferase-aSyn 3′UTR reporter vector (as in FIG. 4 g; along with a Renilla luciferase control), or with this vector modified to encode the rs356165 (C>T) or the rs78991202 (T>G) minor alleles. Dopamine (100 μM) or picrotoxin (100 μM) were added to the culture medium for 24 hrs and luciferase activity was quantified as above and presented as the Firefly/Renilla luciferase ratio. n=6 for each group, *:p<0.05,**:p<0.01, ***:p<0.001, ANOVA followed by Bonferroni post hoc test vs. corresponding vehicle-treatment. e, Predicted local secondary structure of aSyn 3′UTR RNA near the rs356165 and rs78991202 SNPs using RNAfold ³⁰. A predicted miR-34-3p binding site is present in this region (as determined by Targetscan analysis⁶²). Insert shows the predicted global structure of the aSyn 3′UTR, with black box denoting the area of interest. f-g, Left panels: HEK293 cells were transfected with the luciferase-aSyn 3′UTR reporter vector, along with a miR-34b-mimic (f; compared to microRNA mimic control sequences) or with a miR-34b-inhibitor (g; compared to microRNA inhibitor control sequences). Luciferase activity was measured after 24 hrs. n=6 for each group, *:p<0.05,**:p<0.01, ***:p<0.001, ANOVA followed by Bonferroni post hoc test vs. corresponding vehicle-treated for each treatment. Right panels: SH-SY5Y cells were transfected with a miR-34b-mimic (I) or with a miR-34b-inhibitor (g), and total endogenous aSyn protein levels were measured by ELISA (normalized to total aSyn mRNA levels as measured by RT-qPCR). n=5 for each group, *:p<0.05, two-tailed t-test.

FIG. 6. aSyn transcript 3′UTR structure impacts aSyn protein localization. a, In SH-SY5Y cells exposed to dopamine (100 μM) or picrotoxin (100 μM) for 48 h, aSyn protein content is preferentially increased in mitochondrial preparations relative to whole cell aSyn content, as quantified by ELISA. n=5 for each group; *:p<0.05,**:p<0.01, ANOVA followed by Bonferroni post hoc test versus the corresponding vehicle treated cells. b-c, Rat primary cortical neurons cultures at 3 DIV were transfected with a vector encoding a GFP-aSyn fusion protein (green) with either a short (0.3 Kb) or a long (1.1 kb) aSyn 3′UTR and stained with Mitotracker (c, in red) followed by confocal microscopy. Increased colocalization was observed in the context of the longer 3′UTR, both within the axonal growth cone terminal fields (L1 or S1 arrows, magnified in upper inserts) as well as in axonal processes (arrows L2 or S2, magnified in lower inserts). Scale bar, 10 μm in main panel, 5 μm in insets. Colocalization between GFP-aSyn and Mitotracker was quantified by Pearson correlation coefficient in the context of each plasmid transfection, in 12 randomly chosen fields per well. Significance was assessed by Fisher transformation followed by a two-tailed t-test; Error bars are SEM; n>3 wells per condition; *,p<0.05. d, SH-SY5Y cells exposed to dopamine (100 μM) or picrotoxin (100 μM for 48 h) display a reduction in aSyn context within total cell membrane fraction, relative to whole cell protein lysate content, as determined by ELISA assay. n=5 for each group. *, p<0.05; **, p<0.01, ANOVA followed by Bonferroni post hoc test versus corresponding vehicle treatment. e, Rat primary cortical neurons cultures at were transfected with vectors encoding a GFP-aSyn fusion protein (green) with either a short (0.3 Kb) or a long (1.1 kb) aSyn 3′UTR and immunostained for synaptophsyin, followed by confocal microscopy. Colocalization between GFP-aSyn and synaptophysin staining was decreased in the context of the presence of the longer 3′UTR, as quantified by Pearson correlation coefficient between the conditions in individual cells from 12 randomly chosen fields per well. Significance was assessed by Fisher transformation followed by a two-tailed t-test; Error bars are SEM; n>3 wells per condition; *,p<0.05). f, aSyn protein content was quantified by ELISA analysis of mitochondrial protein fractions isolated from 19 human cortical brain samples from unaffected individuals; content was normalized to the total protein concentration, as evaluated by BCA assay. Samples are grouped according to their rs356165 genotype. n=3 for TT genotype, n=12 for GT genotype, and n=4 for GT genotype. Error bars are SEM. *, p<0.05, as evaluated by the gplink assoc function for quantitative traits for the effect of the rs356165 allelic load on mitochondrial aSyn protein concentration. g, Top 5 Gene Ontology categories identified by GSEA analysis to be associated with rs356168 allelic load across 186 unaffected cortical brain samples. See Methods for details. h, A model of aSyn 3′UTR regulation and its consequences. Intracellular dopamine impacts alternative polyadenylation of aSyn transcripts. Generation of the longer aSynL transcript lead to increased translation and prefential localization to mitochondria. PD risk-associated SNPs within the aSynL 3′UTR lead to increased stability of the transcript and thus potentiate protein accumulation.

FIG. 7. Altered aSyn transcript wiring in PD but not other neurological disorders. a, Altered coexpression networks of aSyn transcript isoforms in PD LMD SN neurons. Correlation heat maps of probesets as in FIG. 1 c, but in samples from laser-microdissected nigral dopamine neuron instead of total nigra. Left panel represents the correlation pattern in samples from unaffected individuals, right panel represents samples from PD patients. The probesets displayed are as in FIG. 1 c (those with most significantly altered wiring to the aSyn probeset 204467_s_at). High correlations (r=1) are in red, high anticorrelation (r=−1) in blue and weak correlation in white (r=0). Rows and columns corresponding to correlation with probeset 204467_s_at are bordered with a thick black line. The changes observed in the correlation pattern in the context of PD in LSM SN dopamine neurons are similar to those observed in the full SN samples (FIG. 1 c). b-c, No alteration in co-expression of aSyn probesets in other neurological diseases. aSyn probeset correlations are not altered by schizophrenia or Huntington's disease in the affected tissue. Correlation tables of aSyn probesets (as in FIG. 1 d), in control and Huntington's Disease caudate nucleus brain samples (b, from GEO GSE3790 (12), in control and schizophrenia brain cerebral cortex samples (c, from GEO GSE1761 (13). High correlation (r=1) are in red, weak correlation (r=0) in yellow. No significant changes in correlation between the expression levels of the different aSyn probesets were observed between the disease and control samples.

FIG. 8. aSyn transcript isoforms in PD cerebral cortical and substantia nigra tissue. a, Distribution of the different aSyn 3′UTR isoforms in cerebral cortex samples from unaffected (left) and PD (right) individuals. polyA-RNAseq read count for each isoform is presented as a percentage of total aSyn read count. N=17 individuals for each group (patient or unaffected). Error bars are SEM. b-c, aSynL:total transcript ratio evaluated in SN tissue samples from PD patients or unaffected individuals (b, GEO GSE7621 1, n=10 and 15 for unaffected and PD individuals, respectively) or SN laser microdissected dopamine neurons (c, GEO GSE20141 35, n=8 and 10 for unaffected and PD individuals, respectively). Differences did not reach statistical significance (by two-tailed t-test).

FIG. 9. Significant overlap between GWAS derived PD risk-associated loci and GWAS derived loci that are associated with an elevated aSynL:total transcript ratio. We sought to assess the statistical significance of the observed overlap between GWAS derived PD risk-associated loci (defined by genome-wide significance of p<1×10-3; a total of 384 SNPs; (8)) with GWAS derived loci that are associated with an elevated aSynL:total transcript ratio (defined by genomewide significance of p<1×10-3; a total of 316 SNPs). A total of 22 SNPs rQTL SNPs overlapped with the PD risk SNPs (overlapping loci defined as SNPs that fall within 75 kb of each other). To estimate the chance of occurrence of this many overlapping loci, we performed additional analyses of overlapping loci, but between the previously reported PD risk loci and randomly chosen sets of 316 SNPs (instead of the 316 rQTL SNPs as in FIG. 3 b; we term this ‘bootstrap resampling without replacement’). We performed 5×10⁶ such control analyses of locus overlap using sets of random SNPs. Represented is the frequency distribution of the number of overlapping SNPs found between such random sets of SNPs (316 each) and the PDassociated loci (384 SNPs), over 5×106 trials. Indicated are the number of trials (red) for which a given number of SNPs (black) overlap with the PD-associated loci. With the random SNP intersections, a mean of 2.3 SNPs is observed, and the maximum observed value is 14. This distribution corresponds to the intersection expected simply by chance between 316 random SNPs and the PD associated loci. As we found that 22 rQTL SNPs overlapped with the PD-associated loci, this is significantly higher than one would expect by chance (p<10-6 by the empirical resampling analysis).

FIG. 10. Additional analyses of aSyn transcript isoform ratio regulation. a, GABA receptor but not glutamate receptor modulators alter the aSynL:total ratio. Left panel: aSynL:total ratio as measured by RT-qPCR in primary cortical neurons exposed to the GABA-A receptor antagonist picrotoxin (100 μM), the GABA-A receptor agonist muscimol (100 μM), the glutamatergic receptor agonist NMDA (100 μM), the glutamatergic receptor agonist kainic acid (50 μM), or vehicle. n=5/group, means are represented, error bars are SEM. ***, p<0.001 by two-tailed t-test. Right panel: Human SHSY-5Y neuroblastoma cells were transfected with an expression vector encoding the Firefly luciferase gene fused to the human aSyn 3′UTR (1.1 kb 3′UTR insert; along with a Renilla Luciferase control gene), then exposed for 24 h to picrotoxin (100 μM) or to muscimol (100 μM). Luciferase luminescence is presented as the Firefly/Renilla ratio. n=8/group, mean are represented, error bars are SEM. ***, p<0.001, ANOVA followed by Bonferroni multiple comparison test comparison made: treatments versus vehicle. b, Validation of specificity of in situ hybridization probes (as per FIG. 4 d) detecting either the coding sequences (CDS, thus all human aSyn mRNA isoforms) or specifically long aSyn 3′UTR species. Rat primary cortical neurons cultures at 3DIV were transfected with a vector encoding a GFP-human aSyn fusion protein (green) with either a short (0.3 Kb) or a long (1.1 kb) aSyn 3′UTR and subjected to in situ hybridization with either a probe targeting human aSyn mRNA CDS (red) or a sequence of human aSyn 3′UTR specific to the long 3′UTR transcripts (blue). While no signal was observed for any probe in untransfected cells, cells transfected with the short 3′UTR construct (‘Transf. aSyn Short’, upper panels) exhibit robust red signals but no blue signal; cells transfected with the long 3′UTR Trans aSyn Long’, lower panels) exhibit both red and blue signals. c, Schematic representation of the pulse-chase procedure for nascent RNA isolation. During the pulse period (in blue), ethinyl uridine (EU) is present in the culture medium and is incorporated into the newly transcribed RNA (red). As the pulse period continues, labeled RNA progressively replaces the pre-existing unlabeled RNA (black). During the subsequent chase period, EU is not present in the media, and the newly transcribed RNA is unlabeled (black). At later stages of the chase period, unlabeled RNA (black) progressively replaces the labeled species (red). At different time points during the chase, total RNA is extracted, and from this total population, labeled RNA (red) can be specifically captured and submitted to RT-PCR analysis. d, aSynL:total ratio in nascent RNA upon dopamine treatment in SH-SY5Y cells. Cells were treated with EU for 4 hours, together with either dopamine (100 μM) or vehicle. Cells were immediately harvested and the aSynL:total ratio was evaluated in both the total RNA (left panel) and the captured EU-labeled RNA (nascent RNA) by RT-qPCR. We observe that after 4 h of dopamine treatment, the increase in aSynL:total ratio is robustly observed in the nascent population but not in total RNA. n=5/group, mean are represented, error bars are SEM. *, p<0.05, two-tailed t-test. e, Transcription inhibition suppresses the impact of dopamine treatment on the aSynL:total ratio in SH-SY5Y cells. Cells were treated with combination of dopamine (100 μM) and actinomycin D (10 μg/mL) and harvested after 12 or 24 h. The aSynL:total ratio was evaluated in total RNA by RT-qPCR. We observe that transcription inhibition prevented the dopamine-mediated increase in aSynL:total ratio otherwise observed after 24 h of treatment. n=6/group, mean are represented, error bars are SEM. **, p<0.01, two-tailed test. f, Polyadenylation site disruption mimics and occludes the dopamine-mediated potentiation of the aSynL:total ratio. Human SHSY-5Y neuroblastoma cells were transfected with an expression vector encoding a GFP-aSyn fusion protein with a 1.1 kb aSyn 3′UTR (“Wild-type 3′UTR”, left) or with such a vector that harbors a deletion of the predicted polyadenylation signal sequences utilized for generation of an aSyn transcript with a short 3′UTR (‘disrupted polyA site’, right). Cells were lysed after 48 h, and RNA was extracted and analyzed by Northern blotting using a CDS-specific probe. Upper panel:aSynL:total ratio from Northern blot quantification. n=3/group. Means are represented; error bars are SEM. *, p<0.05, onetailed t-test. Lower panel: representative Northern blot. Dopamine treatment leads to an increase in an aSynL (1070 nt 3′UTR length) transcript relative to a shorter (300 nt 3′UTR length) transcript, both encoded by the exogenous plasmid. In the context of the disrupted polyA site, relative production of aSynL is increased even in the absence of dopamine. g, Nomifensine treatment suppresses dopamine-mediated potentiation of the aSynL:total ratio. Left panel: aSynL:total ratio, evaluated by RTqPCR in rat primary cortical neurons culture. Cells were exposed to combinations of dopamine (100 μM) and nomifensine (100 μM) for 24 h, as indicated, before harvesting and RNA extraction. Mean levels are displayed; errors bars are SEM; n=6 for each group. **:, p<0.01; ***, p<0.001, ANOVA followed by Bonferroni multiple comparison test. Right panel: Human SHSY-5Y neuroblastoma cells were transfected with an expression vector encoding the Firefly luciferase gene fused to a human aSyn 3′UTR (1.1 kb insert; along with a Renilla Luciferase control gene). Cells were then exposed for 24 h to dopamine alone (100 μM) or, dopamine with nomifensine (100 μM), before luminescence measurement. Data are presented as Firefly/Renilla luminescence ratio. n=8 for each group; *, p<0.05; ***, p<0.001; ANOVA followed by Bonferroni multiple comparison test. h, Effect of dopamine agonists on aSynL:total ratio in cultured rat neurons. aSynL:total ratio, evaluated by RT-qPCR in rat primary cortical neurons cultures. Cells were exposed to dopamine (100 μM), 7-OH DPAT (100 μM), Quinpirole (20 μM) or SKF38390 (20 μM) during 24 h before cells harvest and RNA extraction. Mean levels are displayed; errors bars are SEM; n=6 for each group.

FIG. 11. Evidence for translational regulation of aSyn through distal 3′UTR sequences. a, aSynL is preferentially associated with polysomes. aSynL:total ratio evaluated by Affymetrix probesets 204467_s_at and 211546_x_at in total and polysomal-associated RNA from human MCF10A cells (using existing data from GEO GSE11011 ₂₅). The aSynL:total ratio is significantly increased is the polysome fraction, suggesting enhanced translation of the longer 3′UTR aSynL mRNAs. n=6/group; ***, p<0.001, two-tailed t-test. b, Dopamine and picrotoxin treatment do not influence the translation of short aSyn 3′UTR. Human SHSY-5Y cells were transfected with a firefly luciferase-short aSyn 3′UTR (275 nt) or firefly luciferase-long aSynL 3′UTR (1100 nt) reporter vector along with a Renilla luciferase control. Dopamine (100 μM) or picrotoxin (100 μM) were added to the culture medium for 24 hrs and luciferase activity was quantified and presented as the Firefly/Renilla luciferase ratio. n=6 for each group. c, Genomic variants in aSyn 3′UTR that do not affect its translation. Human SHSY-5Y cells were transfected with a firefly luciferase-aSynL 3′UTR reporter vector (as in FIG. 5 d along with a Renilla luciferase control), or with this vector modified to encode the rs34825 (A>G), rs1701607 (C>T), rs35733299 (C>T) or rs35716318 (G>A) minor alleles (see FIG. 5 c). Dopamine (100 μM) or picrotoxin (100 μM) were added to the culture medium for 24 hrs and luciferase activity was quantified as above and presented as the Firefly/Renilla luciferase ratio. n=5 for each group. d, Reduction of intracytoplasmic dopamine by VMAT2 overexpression reduces dopamine effect on aSyn 3′UTR mediated translation. SH-SY5Y cells were co-transfected with an expression vector for VMAT2 (see FIG. 4 f) or vector control, along with a firefly luciferase-aSyn 3′UTR reporter vector and a Renilla luciferase control, and then exposed to dopamine (100 μM) for 48 h. Dopamine treatment potentiates aSyn 3′UTR mediated translation, but this effect is cancelled by VMAT2 overexpression. n=5-6 for each group, errors bars are SEM; *, p<0.05; **, p<0.01; ***, p<0.001. ANOVA followed by Bonferroni post-hoc test versus corresponding vehicle treatment. e, Dopamine and miR-34b affect aSyn translation independently. SH-SY5Y cells were transfected with miR-34b inhibitor or a control inhibitor and treated with dopamine (100 uM) for 24 h or vehicle only. Total endogenous aSyn protein levels were measured by ELISA and normalize to total aSyn mRNA levels measured by RT-qPCR. The respective contribution of each factor (dopamine and miR-34b) as well as their potential interaction was evaluated by fitting the following linear model for aSyn translation in function of dopamine and miR-34, allowing an interaction between both factors (aSyn=a.miR+b.Dopa+c.MirXDopa+d) using R aov function. N>5/group. Results of the fitting process for a and b were highly significant (p=7.4E-4 and 1.9E-3 respectively), confirming the significant increase of aSyn translation by both miR-34b inhibition and dopamine treatment. No interaction between those two factors was however identified (p=0.65); dopamine and Mir-34b effects are additive and thus appear independent. f, Mir-7 impacts the translation of long and short aSyn 3′UTR isoforms equivalently. Human SHSY-5Y cells were transfected with firefly luciferase reporter vectors that harbor no aSyn 3′UTR, aSyn long 3′UTR (1074 nt) or aSyn short 3′UTR (275 nt), as well as Mir-7 mimic or control miRNA mimic (and a Renilla luciferase control). Luciferase activity was quantified as above and presented as the Firefly/Renilla ratio. (n=6 for each group, mean are represented, error bars are SEM. **, p<0.01; ***, p<0.001, ANOVA followed by Bonferroni post hoc test vs. “no 3′UTR” group).

FIG. 12. aSyn transcript 3′UTR isoform impacts aSyn protein translation and protein localization. a-c, Primary cortical neuron cultures were generated from PAC transgenic mice. At day 4 in vitro (DIV), cultures were treated with picrotoxin (100 μM), dopamine (100 μM) or vehicle, for 24 h as indicated. Cultures were then stained with Mitotracker (red) as well as with an antibody specific for aSyn (green). Imaging of cultures was by confocal microscopy. a, White squares denote regions that are magnified in b; arrows in b point to mitochondria signal within a neurite process. c, Colocalization of aSyn and Mitotracker signals was quantified in digital images of 10 randomly chosen fields within each of N>3 independent wells per condition. Means are represented, error bars are SEM. Significance of the effect of drug treatments (versus vehicle) was assessed by Fisher transformation followed by a two-tailed t-test. *, p<0.05; **, p<0.01. d, Mitochondrial enrichment confirmation by Western Blot. Intact mitochondria were purified using the Qproteome mitochondria isolation kit. Total protein (left) and isolated mitochondria protein fractions (right) from two representative brain samples were probed by Western Blotting for TOM20 (upper panel), a mitochondrial protein, or synaptophysin (SYP, lower panel), a synaptic protein. e-f, Human SHSY-5Y neuroblastoma cells were transfected with an expression vector encoding a GFP-human aSyn fusion gene with a short (0.3 Kb, “aSyn-short 3′UTR”) or long (1.1 kb, “aSyn-long 3′UTR”) aSyn 3′UTR, or with GFP only (“Ctl”). e, aSyn protein level was quantified by ELISA in protein extracted from purified mitochondria. aSyn concentration is expressed relative to the total protein concentration as determined by bicinchoninic acid (BCA) assay. n=5 for each group. Means are represented. Error bars are SEM. **:p<0.01, ANOVA followed by Bonferroni post hoc test. f, aSyn protein levels were quantified by ELISA in total protein extracts. aSyn concentration is expressed relative to the total protein concentration as determined by BCA assay. n=5 for each group. Means are represented. Error bars are SEM. g, Schematic representation of the method for assessing the global functional impact of rs356165 on the transcriptome in unaffected cortical brain samples. Left panel: Unaffected individuals are characterized according to their rs356168 risk allele load: 0 for homozygous for the protective allele (AA), 1 for heterozygous (AC) and 2 for homozygous for the risk allele (CC). Using genome-wide expression profiles in cortical brain samples from unaffected individuals, for each gene, the correlation of its expression level with the risk allele load is evaluated across all samples. For instance, Gene 1 expression increases with the risk allele load, and will thus exhibit a correlation value close to 1. By contrast, Gene 3 profile leads to a negative correlation value and Gene 2 to a value close to 0. We next evaluated whether groups of genes belonging to common biological functions are overrepresented among those gene expression profiles that correlate with a one allele or the other. To this end, the correlation values for all gene expression profiles is used as a pre-ranked input for Gene Set Enrichment Analysis (GSEA). Right panel: GSEA output example, with a biological function found to be significantly associated with rs356168 allele load in control brain samples (Mitochondria Membrane Part). The majority of gene expression profiles in this category (vertical black lines) are enriched in the red zone, corresponding to strong correlation with the disease allele. The Enrichment Score is a measure of such overall correlation₃₄. Below are listed the genes (included within the Mitochondria Membrane Part annotation category) whose expression profiles correlate with rs356168 allele load, and thus account for the annotation category enrichment.

FIG. 13. aSynL:total ratio is modified by disease-associated environmental factors. a-c, aSynL:total ratio is increased by mitochondrial toxins. a, Gene expression analysis of brain regions of mice treated daily for 5 days with 30 mg/kg intraperitoneal MPTP or saline (using existing data from GEO GSE7707 ₆₂). The aSynL/total ratio was evaluated as a ratio of the Affymetrix probesets 1418493_a_at and 1436853_a_t). Comparisons were performed for MPTP-treated versus saline controls within each brain region, n=3/group, *, p <0.05, two-tailed t-test. b, Reanalysis of brain gene expression of macaques treated daily with intraperitoneal MPTP hydrochloride (0.2 mg/kg) or saline for either 6 or 12 days (“presymptomatic state”, GEO GSE4550 ₂₈). The aSynL/total ratio was evaluated with Affymetrix probesets 204466_s_at and 211546_x_at, (as the human 204467_s_at poorly detects macaque aSyn mRNA). Comparisons were done for MPTP-treated versus saline controls within each brain region, n=3-6/group; *, p<0.05, two-tailed t-test, (*):p<0.05, onetailed t-test. c, Reanalysis of transcriptome changes in data from human SK-N-MC cells treated with chronic low-dose rotenone or vehicle for one or two weeks (GEO GSE4773 63). aSynL/total ratio was evaluated as a ratio of Affymetrix probesets 204467_s_at and 211546_x_at. Comparisons were done for rotenone versus vehicle for each time point, n=3/group; *, p<0.05, two-tailed t-test; (*), p<0.05, one-tailed t-test. d, Nicotine treatment decreases the expression of an aSynL-3′UTR bearing reporter gene. Luciferase levels in human SY-5Y neuroblastoma cells, transfected with a plasmid encoding a Renilla gene and a luciferase gene fused to the human aSynL 3′UTR (1.1 kb). Combinations of dopamine (100 μM) and nicotine (100 μM) were added, as indicated, to the culture medium immediately after transfection and luciferase activity was measured after 24 h. Mean normalized luciferase Firefly/Renilla levels are displayed; errors bars are SEM; n=6 for each group. Comparisons are made between nicotine treated groups and the associated vehicle treated group.*,p<0.05; ***, p<0.001, two-tailed t-test. e, DJ-1 knockdown increases aSynL:total ratio in human neuroblastomas cells. aSynL:total ratio was analyzed in existing transcriptome data of DJ-1-silenced human SH-SY5Y neuroblastoma cells and control treated cells, measured by Affymetrix Human Genome U133 Plus 2.0 Array. The aSynL:total ratio was quantified using a ratio of expression values for Probesets 204467_s_at and 211546_x_at; GEO GSE17204 ₄₈. Mean levels are displayed; errors bars are SEM; n=4/group; ***, p<0.001, two-tailed t-test. f-g, Aging is associated with an increased aSynL:total ratio in human brain. aSynL:total ratio was quantified in existing postmortem brain sample whole transcriptome data from four different brain regions of healthy donors gathered by age, as measured by Illumina humanRef-8 v2.0 expression beadchip (f, Probes for aSynL and aSyn total are ILMN_(—)1701933 and ILMN_(—)1766165, respectively; data from GSE15745 (49), n=13-17/group) or Affymetrix Human Genome U133 Plus 2.0 Array (g, Probesets for aSynL and aSyn total are 204467_s_at and 211546_x_at, respectively; data from GSE11882 (₅₀). Mean levels are displayed; errors bars are SEM; n=17-25/group. All values are normalized to prefrontal cortex samples from youngest group. Comparisons are made between age groups within each brain region. *, p<0.05; **, p<0.01; ***, p<0.001. ANOVA followed by Bonferroni post hoc test in (f); two-tailed t-test in (g).

FIG. 14. aSynL:total ratio in human tissues. a, aSynL:total ratio in different human brain regions. aSynL:total in postmortem samples from twenty-two different brain regions of healthy donors, grouped by age, measured by Affymetrix Human Genome U133 Plus 2.0 Array (derived from the Human Body Index GEO GSE7307 dataset; see Methods). aSynL and aSyn total expression levels are determined using Probesets 204467_s_at and 211546_x_at, respectively. Mean levels are displayed; errors bars are SEM; n=7-8/group). Values are normalized relatively to the level in Substantia Nigra (in red). b, SynL:aSynT ratio in blood from PD patients and controls. aSynL:total in peripheral blood collected from 18 Parkinson's Disease patients and 12 healthy controls and measured using Affymetrix Exon 1.0 ST Array (GEO GSE18838 ₅₁). The ratio of each CDS and 3′UTR probe to the aSyn whole transcript level (estimated as the average of all probes) for PD patient group (red) is displayed relatively to the control group (black). Mean levels are displayed; errors bars are SEM; n=12-18/group). *, p<0.05, two-tailed t-test. A schematic mapping of the aSyn mRNA (green) regions detected by the probes is shown, with the 3 different 3′UTR probes represented by black boxes as indicated.

FIG. 15 shows GDW analysis with such significant threshold (exactly as in FIG. 1A) or without.

DETAILED DESCRIPTION

SNCA and aSyn are used interchangeably. SNCA Long and aSynL are used interchangeably.

The term “about,” as used herein when referring to a measurable value such as an amount of a compound or agent of this invention, dose, time, temperature, and the like, is meant to encompass variations of +/−20%, +/−10%, +/−5%, +/−1%, +/−0.5%, or even +/−0.1% of the specified amount.

The term “Parkinson disease” (PD) as used herein is intended to encompass all types of Parkinson disease. In some embodiments, the term Parkinson disease means idiopathic Parkinson disease, or Parkinson disease of unexplained origin: that is, Parkinson disease that does not arise from acute exposure to toxic agents, traumatic head injury, or other external insult to the brain. In some embodiment, the invention is directed to detecting or screening for early or late onset Parkinson disease.

The terms dyswired, rewired, unwired and miswired are used interchangeably.

The sequence of SNCA transcripts are known in the art.

The invention is directed to methods to confirm, diagnose, determine predisposition to and/or determine risk of developing PD in a subject. The invention is based on the observation that there is an increase in the SNCA long transcript to SNCA total transcript ratio in a PD patients relative to individuals unaffected by PD.

Various embodiments of the methods of the invention are discussed. The methods can comprise, consist essentially of, or consist of the step which are discussed.

Various kits for use in the methods of the invention are discussed. The kits can comprise, consist essentially of, or consists of the various reagents discussed.

In certain embodiments, the methods include determining SNCA long transcript to SNCA total transcript ratio in a subject's sample, and comparing the subject's ratio to a reference SNCA long transcript to SNCA total transcript ratio. In certain embodiments, the reference ratio can be determined from subjects having non-PD status. In other embodiments, the reference ratio is PD status ratio, which is determined from PD subjects, for example subjects diagnosed to have PD by other means. In certain embodiments the SNCA long transcript to SNCA total transcript ratio in a subject's sample is compared to a reference ratio from subjects having non-PD status, or to a reference PD status ratio determined from PD subjects, or to both non-PD status reference ratio and PD status reference ratio, to determine whether the SNCA long transcript to SNCA total transcript ratio in the subject's sample is similar to the non-PD status reference ratio and the PD status reference ratio.

In certain embodiments, the methods comprise additional step of conducting a physical examination of the subject, or a neurological examination, or any other suitable determination to confirm, diagnose, determine predisposition to and/or determine risk of developing PD in a subject.

The present invention provides a method of identifying a subject with Parkinson disease as having an increased or decreased likelihood of responding effectively to a treatment, for example with a candidate agent to treat PD, comprising: determining SNCA long transcript to SNCA total transcript ratio in a subject's sample in the presence and absence of the candidate agent, and correlating the SNCA long transcript to SNCA total transcript ratio in a subject's sample to the ratio in a test subject effectively responding to a treatment. In certain embodiments, the treatment is a dopamine affecting agent. In certain embodiments, in the presence of the dopamine affecting agents, the SNCA long transcript to SNCA total transcript ratio in a subject's sample decreases, thereby indicating increased likelihood of effective treatment.

In further embodiments, the present invention provides a method of conducting a clinical trial on a plurality of human subjects or patients. Such methods advantageously permit the refinement of the patient population so that advantages of particular treatment regimens (typically administration of pharmaceutically active organic compound active agents) can be more accurately detected, particularly with respect to particular sub-populations of patients. Thus, the methods described herein are useful for matching particular drug or other treatments to particular patient populations for which the drug or other treatment shows any efficacy or a particular degree of efficacy and to exclude patients for whom a particular drug treatment shows a reduced degree of efficacy, a less than desirable degree of efficacy, or a detrimental effect.

treatment shows any efficacy or a particular degree of efficacy and to exclude patients for whom a particular drug treatment shows a reduced degree of efficacy, a less than desirable degree of efficacy, or a detrimental effect.

In general, such methods comprise administering a candidate agent (e.g., active drug or prodrug) or therapy to a plurality of subjects (a control or placebo therapy typically being administered to a separate but similarly characterized plurality of subjects) as a treatment for PD, determining the SNCA long transcript to SNCA total transcript ratio in the plurality of subjects and correlating the correlating with efficacy or lack of efficacy of the test agent or therapy.

In other embodiments, the invention provides methods to evaluate a treatment for PD, the method comprising determining the SNCA long transcript to SNCA total transcript ratio in a sample, wherein the sample is from a cell culture, from an animal model, or from a subject, wherein the sample is obtained in the presence or absence of the treatment for PD, wherein a lowered ratio of SNCA long transcript to SNCA total transcript ratio in the sample in the presence of the treatment compared to the absence of the treatment is indicative of a therapeutic treatment for PD.

Methods to Quantify Nucleic Acids

Methods to quantify nucleic acids from biological samples are known in the art. Any suitable method to quantify nucleic acids from biological samples are contemplated for use in the invention. In a non-limiting embodiment, RT-qPCR is done as described in reference 38. SNCA long to SNCA total ratio were quantified using ΔΔCt using primers pairs HaSynLfw (SEQ ID NO: 1 ATTGAAGTATCTGTACCTGC) HaSynLrv (SEQ ID NO: 2 AAGACCCTGCTACCATGTATTC) and HaSynTfw (SEQ ID NO: 3 AGGGTGTTCTCTATGTAGG) HaSynTrv (SEQ ID NO: 4 ACTGTCTTCTGGGCTACTGC) for human sequence, or RaSynLfw (SEQ ID NO: 5 AACTTCTTGAGAACAGCAACAA) RaSynLrv (SEQ ID NO: 6 CTCCCCTCTCACTACAG) and RaSynTfw (SEQ ID NO: 7 CAACGTGCCCAGTCA) RaSynTrv (SEQ ID NO: 25 GGATGCTGAGGGGCAGGT) for mouse and rat sequences.

Alternatively, for any of the SNCA transcript isoforms to be quantified, suitable primers specific for an isoform may be designed by known methods in the art. In other embodiments, the skilled artisan is able to modify the sequences of the above-described primers by addition and/or deletion of one or a few nucleotide(s) at the 3′ and/or 5′ end, for example but not limited to addition of nucleotides at the 5′ end of a primer.

target sequence, which is bonded to pairs of fluorophore groups or fluorophore/quenchers, such that hybridisation of the probe to its target and the successive amplification cycles cause an increase or reduction in the total fluorescence of the mixture, depending on the case, proportional to the amplification of the target sequence.

Non limiting examples of labeling systems that can be used to carry out kinetic PCR are the TaqMan™ (ABI®), the AmpliSensor™ (InGen), and the Sunrise™ (Oncor®, Appligene®) systems. The skilled artisan can chose amongst these systems or other any other labeling systems.

Apart from the primers and probe sequence, the skilled artisan can use general knowledge concerning quantitative RT-PCR in order to determine the other parameters for performing the method according to the invention, for example but not limited to, cycling parameters, quantification having regard to a housekeeping gene, etc. Examples of such parameters are well known in the art.

In other embodiments, SNCA long to SNCA total ratio can be quantified using nucleic acid microarrays and probes designed to detect specific transcripts. A non-limiting example of determining SNCA long to SNCA total ratio using nucleic acid microarrays is shown in FIG. 14.

Numeric values and/or ranges of fold difference in ratio for at risk subjects, PD subjects and healthy controls can readily be determined.

Any suitable biological sample can be used to determine SNCA long transcript to SNCA total transcript ratio. The biological sample can be taken from body fluid, such as urine, saliva, bone marrow, blood, and derivative blood products (sera, plasma, PBMC, circulating cells, circulating RNA). The biological sample can be taken from a human subject, from an animal, or from a cell culture. The biological sample can be obtained in vivo, in vitro or ex vivo. Non-limiting examples of biological samples include blood, serum, plasma, cerebrospinal fluid, mucus, tissue, cells, and the like, or any combination thereof. In a non-limiting embodiment the biological sample is blood. In a non-limiting embodiment the biological sample is serum. In a non-limiting embodiment the biological sample is plasma. Any suitable method to isolate nucleic acids from biological samples are contemplated for use in the invention. Biological samples for analysis are stored under suitable conditions. In non-limiting examples biological samples are kept at about 4° C. In non-limiting examples biological samples are kept at about −20° C. In non-limiting examples biological samples are kept at about −70-80° C.

Kits

In certain embodiments the invention provides kits to carry out the methods of the invention. The kits comprise reagents to carry out the steps of determining SNCA long transcript to SNCA total transcript ratio, for example but not limited to primers for RT-qPCR, and optionally other reagents for RT-PCR such as suitable polymerases, nucleotide mix, fluorescent dyes, and so forth. The kits comprise instructions to carry out the step of comparing the ratio determined in the subject's sample to a reference ratio so as to determine whether there is a difference between the ratio determined in the subject's sample and the reference ratio. For example a reference ratio is associated with a PD status, or a reference ratio is associated with a non-PD status, wherein in a non-limiting example the non-PD status ratio is based on the ratio determined from healthy controls.

Dopamine Affecting Agents

The main families of drugs useful for treating motor symptoms associated with PD are levodopa, dopamine agonists and MAO-B inhibitors. In certain embodiments, levodopa is combined with a dopa decarboxylase inhibitor or COMT inhibitor. Dopa decarboxylase inhibitors help to prevent the metabolism of L-DOPA before it reaches the dopaminergic neurons, therefore reducing side effects and increasing bioavailability. In non-limiting examples dopa decarboxylase inhibitors are given as combination preparations with levodopa. The COMT enzyme degrades dopamine Inhibitors of the COMT enzyme thereby prolonging the effects of levodopa, when administered in combination with levodopa.

Dopamine agonists that bind to dopaminergic post-synaptic receptors in the brain have similar effects to levodopa.

MAO-B inhibitors inhibit monoamine oxidase-B (MAO-B) which breaks down dopamine secreted by the dopaminergic neurons. Thus, MAO-B inhibitors, for example but not limited to selegiline and rasagiline, increase the level of dopamine in the basal ganglia by blocking its metabolism.

Animal models of PD, including but not limited to toxin-, inflammation-induced and/orgenetically manipulated models are known in the art. See Meredith G E, Sonsalla P K, Chesselet M F. “Animal models of Parkinson's disease progression.” Acta Neuropathol. 2008 April; 115(4):385-98. Epub 2008 Feb. 14.

EXAMPLES Example 1 Transcriptome Wiring Analysis Implicates α-Synuclein 3′UTR Selection in Parkinson's Disease

Common genetic variants in the human population may play a significant role in the pathogenesis of Parkinson's disease (PD) and other neurodegenerative disorders. As the majority of identified PD-associated variants do not alter protein coding, it is presumed that they modify gene expression, although direct evidence for this has been limited. Here we perform global transcriptome differential wiring analysis of PD patient and unaffected control brain tissues and identify a specific transcript isoform of aSynuclein (aSyn) with an extended 3′UTR, aSyn_(L), that exhibits a dramatic correlation pattern change in diseased tissue. Strikingly, aSyn_(L) is even unwired from other aSyn transcripts with shorter 3′UTRs, suggesting a pathogenic role for altered aSyn 3′UTR usage in disease. Consistent with this, a genome-wide association study identifies disease-associated polymorphisms within the aSyn and Parkin loci as key genetic factors in aSyn 3′UTR selection. An additional determinant of aSyn 3′UTR selection is intracellular dopamine content, suggesting a mechanism for the propensity of dopaminergic neuron cell loss in PD patient brain. Finally, we show that differential 3′UTR usage modifies the accumulation and localization of aSyn protein. Taken together, these findings identify a unifying mechanism for PD pathogenesis in the context of genetic and environmental variation.

PD is the most common movement disorder of aging, characterized pathologically by neuronal loss that is particularly prominent among midbrain dopamine neurons (mDN). Whole transcriptome gene expression studies have afforded an unbiased screen of biological pathways that are altered with disease, and have identified specific RNA transcripts differentially expressed (DE) between PD and control brain tissues ¹⁻³. However, a pitfall inherent in such DE approaches is that the majority of alterations detected are likely to be secondary to the disease process, such as cell loss. Further limiting DE analyses, causal ‘master regulators’ may not themselves be differentially expressed during the course of the disease. In an attempt to overcome such limitations, we established a gene expression network analysis tool, termed ‘global differential wiring’ (GDW; see Methods)^(4,5). Briefly, GDW identifies those transcripts that exhibit the greatest and most consistent change in their co-expression correlation (“rewired”) with DE transcripts when comparing panels of healthy control and patient tissue samples. Such transcripts are hypothesized to play a causal role in the disease.

A central role for aSyn in gene expression network perturbations in PD

GDW analysis was performed on an existing gene expression dataset from age-matched unaffected-control and PD patient substantia nigra (SN) tissue (GEO GSE7621)¹. Strikingly, the most highly rewired probeset identified detects an aSyn isoform that harbors a longer 3′-UTR, aSynL (Supplementary Table 1). Replication of the study with independent PD and unaffected SN datasets (GEO GSE8397 ², GSE20292³, GSE20141⁶) again identified aSynL as among the most rewired transcripts, and aSynL ranked first in a combined analysis (FIG. 1 a; Supplementary Table 1). Of note, despite being the most differentially wired, aSyn is not among the most differentially expressed genes between patients and controls (FIG. 1 a, Supplementary Table 6). aSyn has previously been invoked in sporadic PD, as common SNPs in its locus increase PD risk⁷⁻⁹, and intraneuronal inclusions composed of aSyn protein, termed Lewy bodies, typify PD brain pathology ¹⁰. Furthermore, very rare mutations in aSyn as well as triplication of the aSyn gene locus lead to familial inherited forms of PD ^(11, 12).

A post-hoc analysis, aimed at identifying the factors underlying the high DW score of aSynL, revealed that whereas aSynL expression is typically highly correlated with a sub-network of genes across the panel of unaffected controls, expression of aSynL becomes unwired from this sub-network in the disease sample panel, where it is instead wired to a second sub-network (FIG. 1 b-c). The first sub-network is enriched in transcripts that are associated with synaptic and vesicular transport functions and includes dopa decarboxylase (DDC) and vesicle monoamine transporter type 2 (VMAT2; SLC18A2). In contrast, the second is associated with nuclear localization and transcription regulation functions (Supplementary Table 7). The GDW of aSynL in PD midbrain is unlikely to be a trivial consequence of the loss of mDN, as similar findings were obtained with laser-dissected mDN tissue (FIG. 7 a).

Surprisingly, among the transcripts that appeared rewired from aSynL in PD were other aSyn transcripts, as determined using probesets within the protein coding sequences (CDS) of aSyn (such as probeset 211546_x_at, FIG. 1 b). These data suggest a role for aSyn alternative 3′UTR selection. We thus focused further on changes in correlation among aSyn probesets targeting either the 3′UTR or the CDS (FIG. 1 d, Supplementary table 2). Expression of all aSyn transcripts appeared highly correlated among healthy adult brain tissue samples, as expected. In contrast, the correlation between the 3′UTR probesets and the CDS probesets decreased in the PD state in 2 independent datasets (FIG. 1 e). This finding appears to be PD-specific, as we did not observe such aSyn loss of correlation in other neurological diseases including Frontotemporal Dementia (FTD), Huntington's disease (HD) or schizophrenia (FIG. 1 f, FIG. 7 b-c ^(13, 14)).

A PD-associated SNP is predictive of aSyn rewiring even in unaffected controls.

Transcripts that are most highly rewired in the context of disease are hypothesized to play a causal, high-impact role on global gene expression and thus represent candidate disease modifiers. In such a network model, genetic or environmental variations initially modify these ‘master regulator’ or ‘nodal’ genes, leading secondarily to global network perturbations ^(4, 5). We thus investigated the influence of common PD-associated SNPs in the 3′ region of the aSyn locus on aSynL isoform wiring. Importantly, these analyses were performed in individuals not affected by PD, to minimize potential confounding effects of the disease pathology, using a previously reported dataset of genotyped cerebral cortex tissue samples ¹⁵. In cortical brain samples from unaffected individuals, the presence of a common SNP variant associated with increased PD risk (C at rs356168, 3 kb downstream of the aSyn 3′UTR) is correspondingly associated with significantly decreased co-expression correlation (rewiring) between aSynL and a probe detecting all aSyn transcripts (aSynT) (FIG. 1 g). In the context of a global analysis comparing tissue samples homozygous for the risk-associated variant (rs356168 C/C) or homozygous for the protective variant (rs356168 T/T), aSynL expression is found to be globally unwired (in terms of co-expression correlation) from genes functionally annotated as associated with synaptic function, and to be rewired to genes associated with nuclear functions (Supplementary Table 8). In summary, even unaffected individuals harboring an aSyn PD-risk variant display both the aSyn isoform-specific and global transcriptome rewiring patterns of PD. These data argue strongly that the observed patterns are not secondary to cell loss or other aspect of the disease process.

We next sought to characterize more precisely the different aSyn 3′UTR mRNA species in normal and PD human brain. For this purpose, we devised a high-throughput, whole-transcriptome method for sequencing the 3′UTR ends of polyadenylated mRNA transcripts (termed pA-RNAseq; see Methods) in a cohort of 17 unaffected and 17 PD cerebral cortical tissue samples. This revealed 5 aSyn 3′UTR isoforms, with lengths from 290 nt to 2520 nt (FIG. 2 a-b); of these, the 560 nt and 2520 nt forms were predominant. The existence and relative preponderance of these species was further confirmed by Northern Blot (FIG. 2 c). We next hypothesized, based on the GDW analysis above, that aSyn 3′UTR selection might be altered in PD. Comparison of pA-RNAseq profiles from PD and unaffected cerebral cortex samples revealed an increase in the preponderance of the long 3′UTR species (>560 nt) relative to shorter species (<560 nt; FIG. 2 d, FIG. 8 a). Such a relative increase in aSynL was confirmed by qPCR and appears specific for PD, as this is not observed in RNA from amyotrophic lateral sclerosis patient samples (FIG. 2 e). We note that the modified aSyn 3′UTR selection associated with PD patient tissue is detected in cerebral cortex tissue, which typically harbors pathological evidence of the disease process without frank cell loss; thus, this phenotype is unlikely to be a secondary consequence of neurodegeneration. Re-analysis of the aSynL:total ratio in the context of SN (FIG. 8 b) or laser-microdissected SN mDNs (FIG. 8 c) from PD patients or unaffected individuals did not show statistically significant change, perhaps reflecting confounding effects of the late-stage disease pathology in these samples (such as the dramatic loss of dopamine neurons).

To further circumvent potential confounding effects in disease tissue, we quantified the aSynL:total transcript ratio in unaffected brain tissue from individuals with PD risk-associated and protective SNP variants at the aSyn locus. Reanalysis of cortical tissue from unaffected individuals ¹⁶ demonstrated that the risk-associated variant (C at rs356168) was highly predictive of an elevated aSynL:total transcript ratio. This ratio quantitative trait locus (rQTL) effect was reproduced in an independent series of cerebral cortical tissue samples from AD patients ¹⁶. Combination of both datasets also led to a highly significant association (p<10⁻⁶, FIG. 2 f). Taken together, these analyses implicate genetic variants at the SNCA locus as cis-acting modulators of aSyn 3′UTR selection, even in unaffected brain.

GWAS of aSynL:total ratio in cerebral cortex from unaffected controls

We further pursued the regulation of the aSyn rQTL using an unbiased, genome-wide approach by reanalysis of concurrent genome-wide SNP and cerebral cortical gene expression data ^(15, 16). Strikingly, this genome-wide reanalysis identified the same PD risk-associated SNP in the 3′ region of the aSyn locus (rs356168; as in FIG. 2 f) as the most highly correlated with the aSyn mRNA 3′UTR ratio (FIG. 3 a). We then broadly compared genetic loci implicated by the aSyn ratio (rQTL-GWAS) genome-wide analyses with loci previously implicated by PD risk association (risk-GWAS), aiming to identify overlapping loci (other than aSyn) that would be predictive of PD risk as well as the aSyn mRNA 3′UTR ratio. 13 genetic loci were identified that harbor SNPs associated with both disease risk and ratio-QTL SNPs (p<10⁻³ for each; a lower stringency was chosen for each individual association to reduce false-negative calls¹⁷ and as such combined analyses greatly increase statistical power¹⁸; FIG. 3 b-c, and Supplementary Tables 3, 9). The highly significant overlap between trans-acting loci that modify aSynL:total ratio and those associated with PD susceptibility (p<10⁻⁶ by bootstrap analysis [see Methods], with 8-fold more overlapping loci than predicted to be expected by chance; FIG. 9) further supports a role for aSyn 3′UTR selection in the disease pathology. Remarkably, aSyn and Parkin were identified as the most statistically significant loci in the overlap analysis. Furthermore, other loci identified within this list, such as GDNF and GABA-A receptor B2 subunit, have been implicated in PD pathology ¹⁹.

Rare autosomal recessive inherited mutations in Parkin lead to an early-onset form of PD ²⁰, and Parkin is thought to function in part in the regulation of mitochondrial function or integrity ²¹, which appears altered in late-stage PD pathology ²². To more directly evaluate the role of Parkin in modulating aSyn ratio, we investigated the rodent aSyn transcript 3′UTR ratio in mice that are deficient in Parkin ²³. Parkin deficient mice displayed an increased aSynL:total ratio in brain when compared to littermate controls (FIG. 3 d), consistent with a role for Parkin as an upstream determinant of aSynL:total ratio. The species conservation of alternative aSyn 3′UTR regulation by Parkin supports a functional significance.

Dopamine Regulation of aSyn Polyadenylation

Given the pathological evidence for altered aSyn accumulation in PD mDNs, we hypothesized that dopamine could further modulate aSyn 3′ UTR usage, concomitant with genetic regulation as detailed above. We thus queried the regulation of aSyn 3′UTR selection by dopamine in a primary rat cortical neuron culture model. Treatment of these cells with high levels of dopamine (100 μM) led to an increase in the aSynL:total ratio (FIG. 4 a). To examine the role of dopamine content on aSyn transcript regulation in vivo in mDNs, we compared the effect of 1-Dopa on the aSynL:total ratio in mice treated systemically with I-Dopa—which is taken up by mDNs through the dopamine transporter and leads to increased dopamine content. Whereas the aSynL:total ratio appeared significantly increased by I-Dopa treatment in 2-month old control mouse midbrain (DAT-Cre/Dicer^(flox/+)), I-Dopa treatment did not alter the ratio in midbrain tissue from littermates deficient in mDNs (DAT-Cre/Dicer^(flox/flox) mice; ²⁴, FIG. 4 b). Furthermore, the effect of 1-Dopa on the ratio was not apparent in brain regions other than midbrain, such as striatal tissue. We note that this contrasts with the PD risk-associated SNP effect on the transcript ratio described above, which is readily evident in non-dopaminergic neurons, suggesting that the mechanism of dopamine action on the aSyn transcript ratio may be distinct from that of the risk SNP. Data from a publicly available Gene Expression Atlas (GEO GSE7307) further supports an elevated aSyn_(L):total in midbrain dopamine neurons: among 22 human brain regions analyzed, SN exhibits the highest ratio (FIG. 14 a). Screening of other neurotransmitter receptor signaling modulators in vitro also supported a role for GABAergic modulation in the regulation of the aSynL:total transcript ratio. Specifically, the GABA-A antagonist picrotoxin, significantly increased this ratio in cortical primary cultures (FIG. 10 a). In contrast, modulation of NMDA or kainate glutamate receptors did not appear to impact the aSynL:total transcript ratio (FIG. 10 a).

To confirm the modified aSyn 3′UTR usage in an independent fashion, we next performed in situ hybridization (ISH) studies on primary cortical neuron cultures from transgenic mice bearing a fragment of human chromosome 4 encompassing the whole aSyn locus including the 3′UTR ²⁵ (termed aSyn P1 Artificial Chromosome [PAC] mice). Nucleic acid probes were designed to either detect all human aSyn mRNA species or specifically the human long 3′UTR; these probes do not cross-react with endogenous rodent aSyn mRNA (FIG. 10 b). As expected, treatment with either dopamine or picrotoxin led to an increase in the aSyn_(L):total ratio (FIG. 4 d-e).

To characterize the mechanism by which dopamine impacts the aSynL:total ratio, we sought to distinguish between co-transcriptional modifications (acting on nascent aSyn mRNA generation) such as alternative polyadenylation, and post-transcriptional effects on the relative stability of different isoforms. We thus proceeded to perform pulse-chase RNA labeling studies in dopamine treated or untreated human SH-SY5Y cells (FIG. 10 c). Dopamine treatment exclusively during the pulse-labeling period led to a robust and durable increase in aSyn_(L):total ratio among the labeled RNA population. By contrast, dopamine treatment exclusively post-labeling did not produce any effect on the aSyn_(L):total ratio among the labeled RNA population (FIG. 4 c). We also observed that aSyn_(L):total ratio gradually increased as a function of time after labeling, with a rate independent of dopamine treatment (FIG. 4 c). Of note, the dopamine-mediated increase of the aSyn_(L):total ratio in the nascent RNA population was detectable after as little as 4 hrs of treatment, whereas it took much longer treatment for the dopamine effect to become detectable in the total RNA population (at least 16 hrs; FIG. 10 d). Taken together, these data suggest that dopamine acts co-transcriptionally to modify alternative 3′UTR polyadenylation, rather than acting post-transcriptionally on the stability of the mRNA isoforms. Consistent with such a mechanism, treatment with the transcriptional inhibitor, actinomycin D, along with dopamine, prevented the increase in aSyn_(L):total ratio (FIG. 10 e). Furthermore, disruption of a polyadenylation site corresponding to the short 3′UTR within an aSyn mini-gene plasmid occluded the dopamine-mediated increase in the aSyn_(L):total ratio in the mini-gene context (FIG. 10 f).

The regulation of aSyn 3′UTR selection by dopamine may either be a consequence of accumulation of intracellular dopamine, or due to receptor-mediated dopaminergic signaling. We sought to distinguish these mechanisms. As intracellular accumulation of dopamine is greatly facilitated by the dopamine transporter (DAT) in SN neurons but is absent from cortical neurons, we overexpressed DAT in cortical neuron cultures; this significantly increased the sensitivity of primary cortical neurons to dopamine (at 10 μM) with respect to aSynL:total ratio modification (FIG. 4 f-g). In contrast, the monoamine reuptake inhibitor nomifensine suppressed sensitivity to high-dose dopamine (100 μM), supporting a role for intracellular dopamine accumulation through monoamine transporters (Supplementary FIG. 4 g). We cannot exclude additional extracellular roles for dopamine through receptor signaling, but analysis of receptor agonists was inconclusive (FIG. 10 h).

aSynL 3′UTR is associated with increased aSyn translation

3′UTR sequence elements can lead to both positive and negative effects on mRNA accumulation, translation, or stability. Reanalysis of global RNA studies in cultured cells indicated that aSyn_(L) is enriched in the polysomal fraction relatively to total aSyn, consistent with a positive effect of the aSyn 3′UTR on mRNA translation (FIG. 11 a ²⁶). Consistent with this, either dopamine or picrotoxin treatment, previously shown to increase the aSynL:total ratio also significantly increased endogenous aSyn protein levels in SH-SY5Y cells, as quantified by ELISA (FIG. 5 a). Similarly, I-Dopa treatment of 10-mo old human aSyn PAC transgenic mice (as above in FIG. 4 b) significantly increased the accumulation of human aSyn protein in midbrain but not in other brain regions such as striatum or cortex (FIG. 5 b). To further parse the role of the aSyn 3′UTR element, we transfected a luciferase assay vector that harbors a 1.1 kb human aSyn 3′UTR element into SH-SY5Y human neuroblastoma cells (FIG. 5 c). Treatment of vector-transfected SH-SY5Y cells with dopamine led to increased luciferase expression (FIG. 5 d) that was by contrast not observed for a vector harboring only the first 560 bp of human aSyn 3′UTR (FIG. 11 b). Additionally, the GABA-A receptor agonist muscimol decreased luciferase accumulation, whereas the GABA-A antagonist picrotoxin increased this (FIG. 10 a). Taken together, these findings directly implicate the distal part of aSyn 3′UTR that is specific to aSynL transcript as a cis-acting element leading to increased mRNA translation. The dopamine effect is mediated by preferential generation of the aSynL due to alternative polyadenylation, leading secondarily to increased protein translation.

We next used this luciferase assay to study the specific role of intracellular dopamine on aSyn translation activation through the aSyn 3′UTR. As expected—given the impact of intracellular dopamine of the aSyn transcript ratio (FIG. 4 a, b)—the dopamine reuptake inhibitor nomifensine suppressed the increased luciferase accumulation in SH-SY5Y cells transfected with the luciferase-aSyn 3′UTR vector and treated with dopamine as above (FIG. 10 g). Similarly, overexpression of VMAT2-which sequesters dopamine in vesicles and away from other cytoplasmic constituents (FIG. 4 f) and is thus protective ²⁷—also suppressed the dopamine-mediated increase in luciferase accumulation (FIG. 11 d). These data support a specific role for cytoplasmic dopamine in regulation of the aSynL 3′UTR ratio and translation, perhaps as a consequence of mitochondrial disruption as previously described with cytoplasmic dopamine accumulation²⁸. Consistent with this model, in vivo treatment of mice with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)—a mitochondrial toxin that accumulates in dopamine neuron cytoplasm because of selective uptake of its MPP+metabolite through DAT—led to an increased aSynL:total ratio in vivo (FIG. 13 a, b ²⁹).

Common aSyn 3′UTR SNPs are cis-acting modifiers of aSynL translation

We hypothesized that SNPs present within the aSyn transcript 3′UTR and that are associated with PD risk (within the linkage disequilibrium (LD) haplotype block associated with increased PD risk) may play a direct role in aSynL translation regulation by modifying key 3′UTR cis-acting elements ³⁰. We identified 6 candidate SNPs that are present in aSyn 3′UTR and show variability in the population (minor allele frequency >1%; FIG. 5 c). Luciferase assay vector analysis in SH-SY5Y cells revealed that only 2 out of these 6 SNPs—rs356165 and rs78991202-modify dopamine responsiveness of the aSyn 3′UTR (FIG. 5 d, FIG. 11 c). Strikingly, both of these are specific to the aSynL 3′UTR. Furthermore, whereas these SNPs are separated by approximately 80 nt within the primary 3′UTR sequence, RNA secondary structure analysis predicts that both are located within complementary strands of a single stem-loop structural element (FIG. 5 e). We further note that rs356165 is tightly linked (in LD) with the SNP identified in the rQTL analysis above as regulating the aSynL:total ratio (rs356168; Supplementary Table 4b) and is strongly associated with PD risk (Supplementary Table 4a; linkage for rs78991202 is undetermined). Importantly, the protective allele of rs356165 was found to reduce aSyn 3′UTR-mediated translation (FIG. 5 d). Taken together, these data implicate rs356165 as a candidate causative variant within the aSyn 3′UTR.

Scanning for potential cis-acting regulatory modules within the aSyn 3′UTR that could be altered by the SNP variants, we identified a miR-34b binding site that overlaps with the rs356165 and rs78991202 sites ³² (using TargetScan analysis; FIG. 5 e). Co-transfection of HEK-293 cells with a miR-34b-3p precursor, along with a luciferase vector bearing the aSyn 3′UTR, significantly induced the level of the luciferase reporter (FIG. 5 f; relative to a control miRNA precursor). In contrast, transfection of a miR-34b-3p-specific inhibitor significantly decreased luciferase expression (FIG. 5 g; relative to a control miRNA inhibitor). Strikingly, those effects were abolished in the context of constructs harboring either of the 2 SNP variants as above (rs3561165 C>T, rs78991202 T>G). The effects of the miR-34b-3p mimic and inhibitor on aSyn translation were further confirmed in the context of endogenous human aSyn in human neuroblastoma SH-SY5Y cells (Right panels, FIG. 5 f, g). Although miRNAs typically inhibit the stability of targeted mRNAs, other examples of microRNA-mediated translational induction have been described ³⁴. The miR-34b effect appears independent of the dopamine effect, as the effects appear simply additive in SH-SY5Y cells (FIG. 11 b). We note that unlike the miR-34b target site (which is present in aSynL but not short aSyn 3′UTR transcript isoforms), the predicted target sites for other miRNAs previously implicated in the regulation of aSyn, such as miR-7 ³³, are present within the proximal region of the aSyn 3′UTR and thus impact expression of both long and short isoforms equivalently (FIG. 11 c).

aSyn 3′UTR selection modifies the subcellular localization of aSyn protein

We next probed the potential impact of aSyn 3′UTR regulation on aSyn protein accumulation and subcellular localization in primary neurons. Treatment of primary mouse cortical neurons with dopamine or picrotoxin, shown above to increase the proportion of aSynL transcripts, also significantly increased the fraction of aSyn protein that colocalized with mitochondria (FIG. 12 a-c). This was confirmed by biochemical analysis in human SH-SY5Y cells, as dopamine or picrotoxin treatment was associated with an increased proportion of endogenous aSyn protein within mitochondrial fractions (FIG. 6 a). To relate these findings more directly to the aSyn 3′UTR, we transfected vectors encoding a GFP-aSyn fusion gene, bearing either a short or long aSyn 3′UTR (300 and 1100 nt, respectively), into primary rat cortical neuron cultures. Consistent with a regulatory role for the aSyn 3′UTR, expression of transcripts that harbor the 1.1 kb aSyn 3′UTR led to increased aSyn protein co-localization with mitochondria, relative to expression of transcripts that harbor a short 3′UTR (FIG. 6 b-c). Similar transfection experiments in SH-SY5Y cells, followed by biochemical purification of mitochondrial protein fractions, confirmed the preferential mitochondrial accumulation of aSyn protein in the context of long aSyn 3′UTR transcript expression FIG. 12 d-f) Concomitant with mitochondrial relocalization in the context of dopamine or picrotoxin treatment of SH-SY5Y cells, endogenous aSyn protein concentration in the total membrane protein fraction was decreased (FIG. 6 d). Similarly, in primary rat cortical neuron cultures transfected with a GFP-aSyn fusion gene, colocalization with the presynaptic marker synaptophysin was reduced in the context of the longer aSyn 3′UTR (FIG. 6 e). Taken together, these results suggest a preferential mitochondrial localization of aSyn protein produced from the aSynL transcript.

If indeed aSynL leads to the preferential localization of aSyn protein at mitochondria, one prediction would be that such localization would be apparent in human brain tissue from unaffected individuals that harbor the PD risk-associated P allele (as such tissue displays an increased aSynL/Total ratio; FIG. 2 f). Strikingly, aSyn protein concentration in mitochondrial fractions was significantly increased in the context of the aSyn locus SNP risk allele in an allele dose-dependent manner (FIG. 6 f), whereas such an increase was not apparent for total aSyn concentration. A final prediction is that aSyn relocalization to mitochondria might lead to evidence of mitochondrial dysfunction ³⁵, even in brain tissue from unaffected individuals that harbor the PD risk allele. To this end, we identified those transcriptome-wide gene expression changes that are most highly dependent on the allelic load of the PD risk-associated SNP variant across a panel of 183 cortical brain samples from unaffected individuals (see Methods). The set of modified transcripts was then functionally annotated by Gene Set Enrichment analysis (GSEA ³⁶; FIG. 12 f). Among the 7 Gene Ontology categories most impacted by the risk SNP (p<0.01, FDR<25%) the majority relate to mitochondrial function (FIG. 6 g). This is consistent with prior studies of patient-derived PD substantia nigra autopsy tissue using differential expression GSEA analysis ⁶.

Discussion

The identification of disease-associated common genetic variants in GWAS has led to excitement as well as significant controversy over their relevance ³⁷. A particular challenge is to bridge the gap between the observed associations and biological mechanisms. Indeed, such disease associations may be a synthetic consequence of nearby rare mutations, or other variants in LD ³⁸ ³⁰. Our analysis combines GDW and complex QTL analysis to gain sufficient insight and provide a plausible biological mechanism for the role of such variants in sporadic PD.

Our experimental data point to a model of alternative aSyn 3′UTR usage in PD (FIG. 6 h). In this model, dopamine regulates the selection of the polyadenylation site during aSyn transcript maturation and favors the production of a transcript bearing a long 3′UTR. Long aSyn 3′UTR is associated with increased translation and mitochondrial localization of aSyn protein. We provide evidence that risk-associated SNP variants within the long 3′UTR directly modify protein translation; these variants appear to function by interfering with the action of trans-acting regulators such as miR-34b. An additional candidate trans factor is ELAVL4, a gene linked to sporadic PD ³⁹ and that encodes HuD, an RNA binding protein known to alter 3′UTR usage and that appears to bind to aSyn mRNA ⁴⁰. The mechanism by which the long aSyn 3′UTR confers mitochondrial localization of aSyn protein is less clear. We note that 3′UTR-dependant recruitment of mRNAs to the vicinity of mitochondria has been described for other transcripts ⁴¹⁻⁴³.

It is striking that the longer 3′UTR appears to reduce synaptic and increase mitochondrial protein accumulation, a pattern that is reminiscent of the disease state. Furthermore, this shift in protein localization parallels the shift in wiring correlation observed for aSynL expression within either brain tissue of PD patients or unaffected brain from individuals homozygous for a PD-associated variant. An interpretation of these data is that aSyn, normally at the axonal terminal, serves an upstream regulatory or signaling role in determining the expression level of other synaptic function-associated genes. In response to pathological genetic or environmental variation, relocalized aSyn no longer functions in this capacity, but instead impacts the expression of other genes.

We also identified common SNP variants in the aSyn and Parkin loci as regulators of the aSyn transcript ratio. It is of high interest how Parkin may effect this change, and whether this relates to the function of Parkin in mitochondria²¹ ⁴⁴. Elevated intracytoplasmic dopamine as well the MPTP, which increase the aSynL:total ratio, are indeed similarly considered to disrupt mitochondria ⁴⁵. This supports a role for aSyn in mitochondrial toxicity, consistent with the apparent protective effect of aSyn deficiency in the context of mitochondrial toxins ^(46, 47). We hypothesize that, in addition to Parkin, other genes associated with familial forms of PD may be relevant in aSyn transcript 3′UTR selection. DJ-1 is an RNA-binding protein that is mutated in familial autosomal recessive PD ⁴⁸, and re-analysis of gene expression in SH-SY5Y cells deficient in DJ-1 reveals a significant increase in aSyn ratio (FIG. 13 e ⁴⁹).

A major challenge throughout human molecular genetics currently is how to mechanistically pursue SNP associations, particularly from GWAS studies 3. Our goal here is to understand the mechanism and impact of these disease-associated SNPs, and we present a novel approach to do so.

There are two points that relate directly to the choice of SNPs in this Example. The first one concerns the rQTL analysis (FIG. 2) and the second the molecular assays (FIG. 5).

(1) The rQTL analysis is an association study and as such, SNPs are simply markers for specific local haplotypes. The identification of SNPs in GWAS point to an linkage disequilibrium (LD) block (as can be determined based on the HapMap project data) rather than to a single SNP. In other words, looking at one SNP or another in LD would lead to very similar results, as shown in a recent Perspective published in Nature Genetics. See Freedman, M. L. et al. Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet. 43, 513-518 (2011).

Specifically with the analysis and the choice of SNPs: rs356168 was used as a proxy for the SNCA locus 3′ LD region, as identified in the recent GWAS from Simon-Sanchez et al. (2009). The use of such a proxy was justified by the perfect LD (r2=1, d=1) observed between rs356168 and rs2736990—the SNP exhibiting the lowest p-value in the GWAS. The reason why we chose to consider the European GWAS from Simon-Sanchez et al. (2009) to evaluate our proxy was that all the brains used for our rQTL analysis are from Caucasian origin 5. We thus assumed that the results from Simon-Sanchez et al., generated in a population closer to ours than those from Satake et al. (2009) were the more appropriate in our case and mentioned only those for the sake of concision. It could be noted however that rs356168 could also be a very good proxy for the two best SNCA locus SNPs found to be associated with PD in Satake et al (2009), as rs356168 exhibit a strong LD with them in the Japanese panel of HapMap (r2=0.818 and D′=1 for both rs3857059 and rs11931074). These LD considerations are now presented in supplementary table 4.

(2). When querying the potential direct biological role of SNP variants at a molecular level, each SNP needs to be considered independently. We thus tested all previously annotated SNP variants, from the HapMap website at NIH) and 1000 genomes studies with data available at the 1000 genomes project website, that fall within the long 3′UTR candidate region that are also in LD with the PD associated SNPs identified by the GWAS. A total of 2 SNPs met these criteria—rs356165 and rs78991202—and thus we studied both.

We include evidence in vitro and in vivo, as well as in human brain, that the SNPs and the long 3′UTR lead to increased accumulation of mitochondrial aSyn. We do not go on to show that this is pathological, but there are numerous manuscripts to that effect, which we now explicitly cite. Furthermore, simple triplication of the locus can lead to disease, consistent with pathological role for more protein. Finally, we add data showing that, even in unaffected individuals with the SNP that increases disease risk and increases the aSynL:total ratio, there is a specific alteration in the expression of mitochondrial genes. A similar differential expression pattern has been described in end-stage PD.

In addition to the evidence for a genetic link detailed above, non-genetic risk factors associated with PD—such as aging or rotenone exposure (associated with increased PD risk) or nicotine exposure (associated with decreased risk)—predictably modify the aSynL:total ratio (FIG. 13 cdfg ^(37,50,51)). Our data imply that modifiers of the aSynL:total ratio such as the GABA-A receptor agonist muscimol may be of potential therapeutic value (although additional symptomatic effects would limit the utility of GABA-A receptor modulators in late-stage PD). Finally, we note that the aSynL:total ratio is also elevated in gene expression analysis of patient blood samples relative to unaffected controls (FIG. 14 b ⁵²), suggesting utility as a biomarker for disease or treatment.

Methods

Primary Neurons Cultures.

Cultures of rodent neurons were prepared as described in ⁵³. Cells were maintained in vitro for 3-5 days before drug treatments or transfection using Lipofectamine 2000 (Iinvitrogen) following manufacturer's instructions.

Methods to make neurons from human fibroblasts are also known in the art. See for example WO 12/100,083, including but not limited to paragraphs [0215] to [0255], the entire contents of which are hereby incorporated by reference. See also Vierbuchen T, “Direct conversion of fibroblasts to functional neurons by defined factors.” Nature. 2010 Feb. 25; 463(7284):1035-41. Epub 2010 Jan. 27; Ambasudhan et al. “Direct Reprogramming of Adult Human Fibroblasts to Functional Neurons under Defined Conditions” Cell Stem Cell, Volume 9, Issue 2, 113-118, 28 Jul. 2011, the entire contents of which publications are hereby incorporated by reference in their entirety.

Western Blotting.

Western blot analyses were performed as described previously ⁵⁴ with alpha-synuclein antibody (C20, Santa Cruz), Tom20 (Abnova), synaptophysin (Millipore) and β-actin (Abcam, 1:400).

Northern Blotting.

Northern Blots were performed using the NorthernMax kit (Ambion) following manufacturer's instructions. 10 μg of total RNA was purified using miRNeasy kit (Qiagen) and loaded per lane. Probes for Northern blots were generated from a human brain cDNA template by PCR amplification using primers HNBaSynTfw (AGCCATGGATGTATTCATGAAAGGA) SEQ ID NO: 8 and HNBaSynTrv (TTAGGCTTCAGGTTCGTAGTC) SEQ ID NO: 9 for the human aSyn CDS probe, and HNBaSynLfw (GATGTGTTTTATTCACTTGTG) SEQ ID NO: 10 and HNBaSynLrv (AAAAGGCTCAATTAAAAATGTATAAC) SEQ ID NO: 11 for the 3′UTR-specific probe.

aSyn Protein Quantification.

Mitochondria were purified using Qproteome Mitochondria Isolation Kit (Qiagen) and membrane fractions were isolated using Subcellular Protein Fractionation Kit (Pierce) following manufacturers' instructions. Human aSyn protein levels were determined using the aSyn Human ELISA kit (Invitrogen). Absorbance was read on a VersaMax ELISA Microplate Reader (Molecular Devices, Inc) at 450 nm. The amount of human aSyn was normalized to total cellular protein as determined with the DC Protein Assay Reagent kit (Bio-Rad). Mitochondrial preparations were validated by Western blot analysis for Tom20 and synaptophysin (see FIG. 12 d).

In Situ Hybridization.

In situ hybridization were performed using QuantiGene® ViewRNA ISH Cell Assay (Panomics) following manufacturer's instructions, with QG ViewRNA TYPE 8 Probe Sets (Panomics) designed to target either human aSyn CDS sequences (bases 264-634 from NM_(—)000345.3; Panomics) or to target human aSynL 3′UTR sequences (bases 1180-1760 from NM_(—)000345.3).

Nascent RNA Capture.

Total RNA was isolated using a miRNeasy kit (Qiagen) and nascent RNA was purified using the Click-iT® Nascent RNA Capture Kit (Invitrogen) following manufacturer's instructions; total and nascent RNA were then subjected to RT-qPCR analysis as below.

polyA-RNAseq.

RNAseq libraries were constructed essentially as previously described for the NNSR method ⁵⁵ ⁵⁶ with the following modifications. First, the tagged first strand NNSR primer for the reverse transcription reaction was replaced with a tagged, barcoded polyA oligonucleotide mix (TCCGATCTCTNXXXXXXTTTTTTTTTTTTTTTTTTVN (SEQ ID NO: 12; with V=A,C,G mix, N=A,C,T,G mix, and XXXXXX denoting a barcode to allow for subsequent multiplexing of different samples in a single sequencing lane). 100 bp single-end reads were obtained by sequencing of the libraries on an Illumina HiSeq 2000 platform to generate more than 300 million reads for the 34 samples. Data was analyzed using Galaxy ⁵². Reads were mapped using Burrows-Wheeler Alignment tools ⁵⁸.

Immunocytochemistry.

Immunostainings were done as previously described ⁵⁹ with Rabbit anti-aSyn (Santa Cruz, 1:200) or Mouse anti-Synaptophysin (Millipore, 1:100) as primary antibodies, and Alexa 555 goat anti-rabbit IgG or Alexa 633 goat anti-mouse IgG (Invitrogen) secondary antibodies. MitoTracker-Orange (Invitrogen, 1:10000) was added into media for 15-20 min in living cell culture. Collocalization analyses were done in R using EBImage package; using Pearson's correlation coefficient.

In Vivo 1-Dopa Treatment.

2-month old DAT-Cre/Dicer^(flox/flox) and DAT-Cre/Dicer^(flox/+24) or forty-weeks old male PAC-Tg (SNCA)+/−;Snca+/− (a gift from Dr. Robert L. Nussbaum, University of California San Francisco, ²⁵) received 20 mg/kg I-Dopa with 12 mg/kg benserazide (or PBS vehicle only) by intraperitoneal injection daily for 5 days. Benserazide, a DOPA decarboxylase inhibitor that does not cross the blood-brain barrier, was used in combination with I-Dopa as it is with PD patients, to prevent I-Dopa decarboxylation outside of the brain. 1 hour after the last dose, mice were anesthetized by inhaled isoflurane and the brains rapidly removed. The prefrontal cortex, striatum and midbrain were dissected out and stored at −80° C.

Quantitative Real-Time RT-PCR.

RT-qPCR analyses were performed as described ⁶⁰. The human aSynL:Total mRNA ratio was quantified in terms of AACt ⁶⁰ using primer pair Lh for the human long form (HaSynLfw [CTGACACAAAGGACAAA] SEQ ID NO: 13, and HaSynLry [TTCCGAGTGTAGGGTTAATGTT]) SEQ ID NO: 14 and primer pair Th for human total (HaSynTfw [AGGGTGTTCTCTATGTAGG] SEQ ID NO: 15 and HaSynTrv [ACTGTCTTCTGGGCTACTGC] SEQ ID NO: 16). For analysis of either mouse or rat, primer pairs mrL (RaSynLfw [AACTTCTTGAGAACAGCAACAA] SEQ ID NO: 17 and RaSynLrv [CTCCCCTCTCACTACAG] SEQ ID NO: 18) and mrT (RaSynTfw [CAACGTGCCCAGTCA] SEQ ID NO: 19, RaSynTry [GGATGCTGAGGGGCAGGT] SEQ ID NO: 20) were used.

Luciferase Assays.

The human SH-SY5Y neuroblastoma cell line (ATCC) was cultured following the distributor's instructions. Cells were plated at a density of 4×10⁵ cells per well (in 48-well plates) in wells coated with 0.1% gelatin (Specialty Media, Millipore) 24 hours prior to transfection. Transfections were performed with Lipofectamine 2000 reagent (Invitrogen) following the manufacturer's instructions. The human HEK-293T cell line (ATCC) was cultured in DMEM (Invitrogen) supplemented with 10% FBS (Invitrogen). Cells were plated at a density of 8×10³ cells per well (96-well plates). Mir-34b-3p precursor, specific Anti-miR Mir-34b-3p inhibitor, Anti-miR Negative Control #1, and Pre-miR Negative Control #1 were purchased from Ambion. Cells were co-transfected with luciferase reporter plasmids and a small RNA or inhibitor (as indicated) using siPort NeoFx reagent (Ambion) following manufacturer's protocol. Luciferase and Renilla activities were measured 24 h or 48 h after transfection using Dual-Glo luciferase assay system (Promega).

Plasmids

Dual hRen/hLuc pEZX-MT01 plasmid with the first 1074 bp (“Long”, HmiT017582-MT01) or 560 bp (“Short”, HmiT017583-MT01) of human aSyn 3′UTR downstream of luciferase or control vector (CmiT000001-MT01) were purchased from Genecopoeia. Point mutant corresponding to rs356165 C>T and rs78991202 A>C were generated from HmiT017582-MT01 by site-directed mutagenesis (Genewiz). Plasmids expressing a GFP-aSyn fusion with either a long (1074 bp) or a short (560 bp) 3′UTR were generated by insertion in a pEGFP-C1 vector (Clontech) between its XhoI and HindIII restriction sites of HindIII/XhoI digested PCR products obtained from human brain cDNA using the forward primer XhoI-Start (ATCTCGAGCCATGGATGTATTCATGAAAGGA SEQ ID NO: 21) with either HindIII-275 (CAAAGCTTAGGTGTTTTTAATTTGTTTTAACATCGT SEQ ID NO: 22) or HindIII-1074 (CAAAGCTTCATGGTCGAATATTATTTATTGTCAGAA SEQ ID NO: 23) as a reverse primer. PolyA-disrupted vector was generated from pEGFP-aSyn-Long 3′UTR; the putative polyadenylation signal at position 542 to 552 of the aSyn 3′UTR “AATTAAAATAA” SEQ ID NO: 24 was deleted by site directed mutagenesis (Genewiz).

Human Autopsied Brain Samples.

Age-matched samples from Parkinson's disease patients (5 female, 12 male, average age 78.29±5.95), unaffected individuals (5 female, 12 male, average age 74.05±13.04) or ALS patients (7 female, 9 male, average age 70.02±11.01) BA9 area brain samples were obtained from the New York Brain Bank ⁶¹. Samples were provided devoid of any personal information.

Statistical Analysis.

Results are given as mean±S.E.M. Where appropriate, statistical analysis were performed with analysis of variance (ANOVA) test followed by Bonferroni corrected tests. Otherwise, comparisons between groups were conducted using Student's t test.

QTL Analysis.

Data from cerebral cortex transcriptome-wide gene expression analyses, as well as genome-wide SNP analyses for the same 188 individuals, were previously described ¹⁶. These data were obtained from the Laboratory of Functional Neurogenomic at the University of Miami School of Medicine, and reanalyzed. The rQTL for each sample was determined as a ratio of the value for probes GI_(—)6806896-I and GI_(—)6806897-A. Subsequently, the rQTL value was provided as a continuous numeric trait variable in the gplink ⁵⁵ assoc function, filtering for minor allele frequency below 0.05, genotype missingness above 0.1 and Hardy-Weinberg equilibrium threshold of 0.001. Haploview was used to generate a Manhattan plot of the output data. For loci intersection analysis as in FIG. 3 b, the output of the rQTL analysis was queried at SNPs previously reported to be associated with PD risk (p-value<10⁻³) in GWAS analysis of individuals from a European ancestry ⁹. This GWAS data for PD risk were taken directly from the results presented in the supplementary data of Simon-Sanchez et al. We considered the European GWAS from Simon-Sanchez et al. for the intersection as the brains used for our rQTL analysis are from Caucasian origin ¹⁶. Resampling analysis were done in R: To assess the statistical significance of the intersection, a resampling without replacement procedure was done using R by selecting 316 SNPs out of the one used in the rQTL study. The number of SNPs whose 75 kb radius locus overlap with the PD-associated loci is evaluated. This process is repeated 5 million times and the results obtained from the actual data are compared to the random distribution generated.

Differential Wiring Analysis.

Datasets were downloaded from the Gene Expression Omnibus website of the National Center for Biotechnology Information at the NIH; specific dataset identification numbers are provided in supplementary table 5. All subsequent data manipulations and analyses were done using R Bioconductor package. Correlations between gene expression levels were assessed using cosine similarity on log-transformed levels; briefly, two genes whose expression levels are simultaneously high or low across many samples are in phase and will have a correlation coefficient close to 1. On the contrary, if one gene shows high expression levels when another one shows low across many samples, those two genes are in anti-phase and will have a correlation coefficient close to −1. The absence of linear relationship between the expression levels of both genes will result in a correlation coefficient close to 0. Comparisons between correlations obtained in two independent groups were done using a Fischer's Z transformation followed by a statistical test using pnorm R function.

The principle underlying DW algorithms ^(4, 5) is that for a given candidate ‘master regulator’ node gene X, the global DW score—when comparing two experimental conditions 1 and 2—is the sum of DW subscores between gene X and each of the other genes Gi queried. The subscore between the gene of interest X (for which the DW score is calculated) and a gene Gi is proportional to:

(i) the extent of the shift in correlation between the expression levels of Gi and X when comparing conditions 2 and 1 (thus genes exhibiting a high number of strong shifts in correlation with many other genes are assumed to be relevant nodes in the differential gene expression network between conditions 1 and 2);

(ii) the extent of differential expression of Gi between conditions 1 and 2 (averaged across the panel of samples for each condition; thus, the more a gene is on average differentially expressed between 2 conditions, the more it is predicted to have a phenotypic impact);

(iii) the level of expression Gi (a more highly expressed gene is thought to have a higher phenotypic impact; this is to compensate for the fact that lowly expressed genes are more likely to exhibit strong shifts in expression between the two conditions).

The two main modifications we introduce to the previously described wiring algorithms ^(4, 5) are: (i) We broadened the analysis of possible ‘master regulator’ genes from only annotated transcription factors to all genes, (ii) We introduced significance threshold tests for the interactor genes: as we included all the genes as candidate ‘master disease regulators’, instead of only all the annotated TF we wanted to avoid artificial results when working at a genome-wide scale than with hundreds of selected genes. Low-selective threshold (p-value=0.05) were however chosen to keep a high sensitivity.

The differential wiring score for a gene X between two experimental groups (1 and 2 with respectively n1 and n2 elements) was thus calculated as the sum over all the genes Gi of the absolute value of the product of:

(i) the conditional Z-distance evaluating the difference observed between the two groups for the correlation between the expression levels of genes X and Gi (<Δ_(Gi 1vs2)>_(p) in the formal DW formula below). Thus, for a given threshold p-value (0.05 here), it has a null value if the correlation shift is not significant. The amplitude of the Z-distance is proportional to the shift in correlation between the two experimental conditions. Fischer's Z-transformation corrects for the non-normal distribution of the correlation value (between −1 and 1). As a consequence, a shift in correlation form 0.7 to 0.9 will lead a Z-distance value higher than a shift from −0.1 to 0.1.

(ii) the conditional log-scaled amplitude of the differential expression of gene Gi (<δ(X, G_(i))_(1vs2)>_(p) in the DW formula below). For a given threshold p-value (0.05 here), it has a null value if the gene is found to not be differentially expressed between the two conditions. If the gene is differentially expressed for the chosen p-value, the value will be the log of the ratio between the averaged gene expression levels in each group.

(iii) the averaged expression level of gene Gi among all samples ((E_(Gi))_(1u2) in the formula below).

As a consequence of the use of significance threshold tests, only those genes which are differentially expressed between the two experimental conditions, and that see their correlation with gene X significantly changed between the two experimental conditions, will participate in the DW score.

Formally, the DW score was thus calculated as:

Differential wiring score for gene X:

DW(X)_(1vs2)=Σ_(G) _(i) |(Δ_(G) _(i) _(1vs2)<δ(X,G _(i))_(1vs2)>_(p)| (E _(G) _(i) )_(1∪2)

With:

${\langle\delta_{1\; {vs}\; 2}\rangle}_{p} = \left\{ {{\begin{matrix} \delta_{1\; {vs}\; 2} & {{{if}\mspace{14mu} {{pnorm}\left( \delta_{1\; {vs}\; 2} \right)}} < p} \\ 0 & {{{if}\mspace{14mu} {{pnorm}\left( \delta_{1\; {vs}\; 2} \right)}} \geq p} \end{matrix}\mspace{14mu} {Conditional}\mspace{14mu} Z\text{-}{distance}\mspace{14mu} {for}\mspace{14mu} a\mspace{14mu} p\text{-}{value}\mspace{14mu} p{\delta \left( {X,G} \right)}_{1\; {vs}\; 2}} = {\frac{{F_{z}\left( {r\left( {X,G} \right)}_{1} \right)} - {F_{z}\left( {r\left( {X,G} \right)}_{2} \right)}}{\sqrt{\frac{1}{n_{1} - 3} + \frac{1}{n_{2} - 3}}}\mspace{14mu} Z\text{-}{distance}\mspace{14mu} {between}\mspace{14mu} {r\left( {X,G} \right)}_{1}\mspace{14mu} {and}\mspace{14mu} {r\left( {X,G} \right)}_{2}}} \right.$

r(X, G)₁, r(X, G)₂ correlation coefficient between the expression levels of genes X and G, evaluated in experimental groups 1 (n1 elements) and 2 (n₂ elements).

${F_{z}(r)} = {\frac{1}{2}{\log \left( \frac{1 + r}{1 - r} \right)}\mspace{14mu} {Fischer}^{\prime}s\mspace{14mu} z\mspace{14mu} {transformation}\mspace{14mu} {for}\mspace{14mu} a\mspace{14mu} {correlation}\mspace{14mu} {coefficient}\mspace{14mu} r}$ ${\langle\Delta_{G\; 1\; {vs}\; 2}\rangle}_{p} = \left\{ {\begin{matrix} {{{\log \left( \frac{\overset{\_}{\left( E_{G} \right)_{1}}}{\overset{\_}{\left( E_{G} \right)_{2}}} \right)}\mspace{14mu} {if}\mspace{14mu} {p.{value}}\; \left( {t.{{test}\left( {\left( E_{G} \right)_{1},\left( E_{G} \right)_{2}} \right)}} \right)} < p} \\ {{{if}\mspace{14mu} {p.{{value}\left( {t.{{test}\left( {\left( E_{G} \right)_{1},\left( E_{G} \right)_{2}} \right)}} \right)}}} \geq p} \end{matrix}\mspace{14mu} {conditional}\mspace{14mu} {DE}\mspace{14mu} {amplitude}\mspace{14mu} {of}\mspace{14mu} {Gi}} \right.$

(E_(G))_(i): collection of the expression level values for gene G among the experimental group 1 All calculations were performed using the R statistical environment.

Two conceptual aspects differentiate the wiring approach used in this study from previous wiring analyses. Hudson, N.J., Reverter, A. & Dalrymple, B. P. A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLoS Comput Biol 5, e1000382 (2009); Reverter, A., Hudson, N.J., Nagaraj, S. H., Perez-Enciso, M. & Dalrymple, B. P. Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data. Bioinformatics 26, 896-904 (2010). We expanded the scope of the potential network nodes (“master regulators”) to all genes, rather than only transcription factors (TF). Our strategy was motivated first by the knowledge that PD and other neurodegenerative disorders are not likely to be primarily due to modification of transcription factors. The identification of aSynL as the top result would not have been possible if we limited to annotated TFs. But more generally: among the (50) most highly ranked GDW genes in our analysis, fewer than 10% are annotated TFs. Thus our finding with aSynL is not an exceptional case. We believe that the network properties underlying the DW approach are not limited to TFs. 2) We hypothesized that a heterogeneous, sporadic human disease would be amenable to this technique.

A previous study did use a wiring network approach to correctly identify the extreme rewiring of a ‘master regulator’ gene transcript in the context of an inherited coding mutation in that gene in cattlel (leading to dysfunction of the TF). But ‘sporadic’ PD is not thought to be a consequence of such a unique coding mutation. We nonetheless reasoned that global wiring analysis would be sensitive enough to detect extreme alterations in the wiring of ‘master regulator’ transcripts that are functionally altered in other ways—even in the absence of an inherited coding mutation, and even in a heterogeneous disease and tissue. We further surmised that such dysfunction/rewiring, in the absence of coding mutations, may be due to altered regulation at the transcription or posttranscription level. For instance, altered gene expression may be imparted by synonymous (non-coding) PD risk-associated SNPs; whereas, dysfunction in the context of post-transcriptional modifications (such as misfolding) may be due to environmental insults such as implicated in PD, including toxins. A more technical aspect of our repurposing of the wiring network approach is also relevant. Given the inherent variability in post-mortem human brain tissue analysis, and the scale of any whole-transcriptome network approach, we decided to include statistical thresholds in terms of whether or not to consider any individual transcript-to-transcript correlation as signal or noise; very weak connections were then discarded (because the sum of many such weak erroneous connections would potentially incorrectly bias the analysis; see Methods for details). To illustrate this last point more directly we reproduced the GDW analysis with such significant threshold (exactly as in FIG. 1A) or without. The use of thresholds greatly sharpens the contrast between the top results and others; however in this analysis aSyn is still on top, which is a reassuring sign that our ultimate finding is not strictly due to the threshold testing. FIG. 15.

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AppendixA: Supplementary Tables 1-9

APPENDIX A

SUPPLEMENTARY TABLE 1 Global differential wiring results

Top 25 probesets identified by the initial GDW analysis of PD vs Ctl in SN samples (a) of PD vs Ctl SN and SN laser-microdissected neurons samples (b) and by the combination of both analysis. For each analysis, the maximum score was set to one. For each table, the score for the analysis of interest is in black, and the score of the same probeset in the two other analysis in indicated in grey as an information. Highlighted in red and orange (Plekhb2) are the two genes (aSyn and Plekhb2, respectively) that appear as top-ranking for each of the analysis.

SUPPLEMENTARY TABLE 2 Genomic coordinates (hg18) of the Affymetrix and Illumina aSyn probes Probe Chr. Strand start stop 207827_x_at 4 — 90962438 90975855 211546_x_at 4 — 90869367 90975803 204466_s_at 4 — 90866502 90866801 204467_s_at 4 — 90865759 90866067 GI_6806896-I 4 — 90866611 90866660 GI_6806897-A 4 — 90869395 90869444

SUPPLEMENTARY TABLE 3 Loci associated to PD and aSyn ratio Combined Position Gene(s) p-value chr4: 90818453-91028750 SNCA 6.48E−15 chr6: 162558416-162618882 PARK2 8.54E−09 chr6: 148905000-149036593 SASH1 1.20E−08 chr20: 16612675-16681299 SNRPB2 1.73E−08 chr7: 47984125-48127326 SUNC1/HUS1/UPP1 2.03E−08 chr5: 160563131-160587671 GABRB2 3.30E−08 chr5: 37874300-37877141 GDNF 3.81E−08 chr15: 36900712-36989378 RASGRP1 4.98E−08 chr12: 25041441-25152643 LRMP 6.61E−08 chr4: 24491750-24554434 CCDC149/LGI2/SOD3 8.28E−08 chr19: 1925313-1955168 CSNK1G2/BTBD2/MKNK2 9.60E−08 chr15: 90636309-90775680 ST8SIA2 9.96E−08 chr8: 136969530-137050409 KHDRBS3 1.31E−07

SUPPLEMENTARY TABLE 4 PD-associated SNPs linkage disequilibrium and frequencies. a SNP OR 95% C.I. rs2736990 1.25 [1.20, 1.30] rs356165  1.33 [1.21, 1.46] rs356168  1.21 [1.06, 1.38] b rs2736990 rs356165 rs356168 rs2736990 x 0.817 1 rs356165  31655 x 0.817 rs356168  4110 27545 x a: Allelic variants associated to PD by PDGene meta-analysis ²². rs2736990 is the SNP found to be the most-associated to PD risk in two GWAS ^(6, 8). rs356168 was found to be the SNP most-associated to aSynL:total ratio in human brain cortex in our analysis (FIG. 3). Rs356165 is located in aSyn 3′UTR and was found to regulate its translation in response to dopamine (FIG. 5). b: Linkage disequilibrium between the 3 aSyn locus SNPs of interest, evaluated using SNAP ⁵⁰ in the HapMap CEU panel (Upper Right, Red); genomic distance in bp (Lower Left, Blue)

SUPPLEMENTARY TABLE 5 GEO datasets used for the study GEO dataset(s) Description Use Figure(s) Reference GSE7621 PD and unaffected SN tissue PD vs Ctl GDW analysis 1ace 1 aSynL: total ratio in PD vs Ctl SN 52b GSE8397 PD and unaffected SN tissue PD vs Ctl GDW analysis 1a 2 GSE20292 PD and unaffected SN tissue PD vs Ctl GDW analysis 1a 3 GSE20141 PD and unaffected LMD mDN PD vs Ctl GDW analysis 1ae S1a 6 aSynL: total ratio in PD vs Ctl LMD SN mDN 52c GSE13152 FTD and unaffected brain cortex aSyn probesets coexpression in FTD 1f 63 GSE3790 HD and unaffected caudate nucleus aSyn probesets coexpression in HD 51b 13 GSE17612 Schizophrenia and unaffected brain cortex aSyn probesets coexpression schizophrenia 51a 14 GSE15222 Genotyped unaffected (and AD) brain cortex aSyn probesets coexpression and ratio in function 1g, 2f 16 of rs356168 aSynL: total rQTL analysis 3abc rs356168 global impact in unaffected individuals 6g GSE11011 polysome associated and non-associated aSyn probesets differential translation 55a 26 RNA from MCF10 cells GSE7707 MPTP-treated mice brain tissue Mitochondrial toxin increases aSynL: total ratio 57a 64 GSE4550 MPTP-treated macaque brain tissue Mitochondrial toxin increases aSynL: total ratio 57b 29 GSE4773 Rotenone-treated SX-N-MC cells Mitochondrial toxin increases aSynL: total ratio 57c 65 GSE17204 Dj-1 knock-down in SH-SYSY cells DJ-1 knock-down increases aSynL: total ratio 57e 49 GSE15745 unaffected brain samples aging increases aSynL: total ratio in brain samples 57f 50 GSE11882 unaffected brain samples aging increases aSynL: total ratio in brain samples 57g 51 GSE7307 unaffected brain samples aSynL: total ratio in different brain regions 58a x GSE18838 Blood samples from PD and unaffected aSynL: total ratio is increased in PD vs unaffected 58b 52 individuals blood

SUPPLEMENTARY TABLE 6 This file contains the list of probesets differentially expressed in PD vs unaffected SN samples (GEO GSE7621) that show an fold change superior to 1 (absolute value on a log scal) and a pvalue <5.10e−2. Diff_Expr PD vs Ctl Relative ProbeSet Gene Locus (log2) Expre level 204338_s_at RGS4 chr1q23.3 −4.14 1.89E−01 213920_at CUX2 chr12q24.11-q24.12 −2.45 9.74E−03 205857_at SLC18A2 chr10q25 −2.40 4.07E−02 205311_at DDC chr7p12.2 −2.19 1.17E−02 210454_s_at KCNJ6 chr21q22.1|21q22.13-q22.2 −2.06 1.49E−02 206836_at SLC6A3 chr5p15.3 −2.04 5.20E−02 205825_at PCSK1 chr5q15-q21 −2.04 7.15E−03 216086_at SV2C chr5q13.3 −1.99 6.01E−02 212224_at ALDH1A1 chr9q21.13 −1.89 5.38E−02 211421_s_at RET chr10q11.2 −1.87 1.34E−02 206935_at PCDH8 chr13q14.3-q21.1 −1.86 5.98E−03 208427_s_at ELAVL2 chr9p21 −1.85 4.10E−03 205110_s_at FGF13 chrXq26.3 −1.83 2.50E−02 208319_s_at RBM3 chrXp11.2 −1.77 8.04E−03 204337_at RGS4 chr1q23.3 −1.65 3.05E−02 215342_s_at RABGAP1L chr1q24 −1.64 6.64E−03 203282_at GBE1 chr3p12.3 −1.60 2.25E−02 214230_at CDC42 chr1p36.1 −1.60 1.37E−02 203476_at TPBG chr6q14-q15 −1.58 1.17E−02 212092_at PEG10 chr7q21 −1.57 1.24E−02 208175_s_at DMP1 chr4q21 −1.55 6.12E−04 204667_at FOXA1 chr14q12-q13 −1.51 4.72E−03 219572_at CADPS2 chr7q31.3 −1.51 2.83E−02 205551_at SV2B chr15q26.1 −1.50 2.60E−02 219895_at FAM70A chrXq24 −1.50 2.51E−02 204364_s_at REEP1 chr2p11.2 −1.46 4.15E−02 220030_at STYK1 chr12p13.2 −1.41 6.49E−04 34726_at CACNB3 chr12q13 −1.40 1.08E−02 204621_s_at NR4A2 chr2q22-q23 −1.36 4.86E−03 204365_s_at REEP1 chr2p11.2 −1.34 2.65E−02 215303_at DCLK1 chr13q13 −1.33 7.33E−03 220559_at EN1 chr2q13-q21 −1.32 7.64E−03 213938_at ERC2 chr3p14.3 −1.31 1.89E−02 214841_at CNIH3 chr1q42.12 −1.31 2.70E−03 213913_s_at TBC1D30 chr12q14.3 −1.31 5.45E−03 203999_at SYT1 chr12cen-q21 −1.30 1.02E−01 213967_at RALYL chr8q21.2 −1.30 1.82E−02 219073_s_at OSBPL10 chr3p22.3 −1.27 7.59E−03 206343_s_at NRG1 chr8p12 −1.27 2.18E−03 203797_at VSNL1 chr2p24.3 −1.26 2.03E−01 205968_at KCNS3 chr2p24 −1.25 5.80E−03 207958_at UGT2A1 /// chr4q13 /// −1.25 1.74E−03 UGT2A2 chr4q13.3 215014_at KCND3 chr1p13.3 −1.24 1.06E−02 209254_at KLHDC10 chr7q32.2 −1.23 4.65E−03 206091_at MATN3 chr2p24-p23 −1.23 3.41E−03 212979_s_at FAM115A chr7q35 −1.22 2.32E−02 205691_at SYNGR3 chr16p13 −1.21 5.29E−02 205389_s_at ANK1 chr8p11.1 −1.20 2.31E−03 216248_s_at NR4A2 chr2q22-q23 −1.19 8.20E−03 214811_at RIMBP2 chr12q24.33 −1.19 6.49E−03 205391_x_at ANK1 chr8p11.1 −1.19 1.11E−02 206382_s_at BDNF chr11p13 −1.19 4.00E−03 214589_at FGF12 chr3q28 −1.18 2.59E−03 208352_x_at ANK1 chr8p11.1 −1.18 1.20E−02 214848_at — — −1.18 6.23E−03 205257_s_at AMPH chr7p14-p13 −1.17 1.48E−02 209560_s_at DLK1 chr14q32 −1.16 6.54E−03 206984_s_at RIT2 chr18q12.3 −1.16 1.36E−02 214930_at SLITRK5 chr13q31.2 −1.16 5.12E−03 205632_s_at P1P5K1B chr9q13 −1.15 1.56E−02 266_s_at CD24 chr6q21 −1.14 6.92E−03 200810_s_at CIRBP chr19p13.3 −1.13 7.13E−02 205348_s_at DYNC1I1 chr7q21.3-q22.1 −1.13 4.31E−02 201340_s_at ENC1 chr5q12-q13.3 −1.13 3.43E−03 210123_s_at

7A /// chr15q13.1 /// −1.13 2.73E−03 CHRNA7 /// chr15q14 LO

204675_at SRD5A1 chr5p15 −1.13 5.56E−03 204260_at CHGB chr20pter-p12 −1.12 2.05E−02 204723 at SCN3B chr11q23.3 −1.11 1.00E−02 206502_s_at INSM1 chr20p11.2 −1.10 3.88E−03 219736_at TRIM36 chr5q22.3 −1.10 1.22E−02 205413_at MPPED2 chr11p13 −1.10 7.42E−03 219603_s_at ZNF226 chr19q13.2 −1.10 9.72E−03 218807_at VAV3 chr1p13.3 −1.10 1.51E−02 208353_x_at ANK1 chr8p11.1 −1.09 1.19E−02 204471_at GAP43 chr3q13.1-q13.2 −1.07 4.56E−02 203680_at PRKAR2B chr7q22 −1.07 1.55E−02 214156_at MYRIP chr3p22.1 −1.07 1.12E−02 207869_s_at CACNA1G chr17q22 −1.07 2.59E−03 213832_at KCND3 chr1p13.3 −1.06 4.34E−02 219855_at NUDT11 chrXp11.22 −1.06 5.35E−03 206014_at ACTL6B chr7q22 −1.06 1.12E−03 203290_at HLA-DQA1 chr6p21.3 −1.06 3.15E−03 204604_at PFTK1 chr7q21-q22 −1.06 3.02E−02 204339_s_at RGS4 chr1q23.3 −1.05 7.21E−03 204622_x_at NR4A2 chr2q22-q23 −1.05 9.28E−03 209755_at NMNAT2 chr1q25 −1.05 1.17E−02 207087_x_at ANK1 chr8p11.1 −1.05 1.10E−02 213484_at — — −1.05 2.09E−02 205377_s_at ACHE chr7q22 −1.05 4.74E−03 221727_at SUB1 chr5p13.3 −1.04 1.76E−02 203498_at RCAN2 chr6p12.3 −1.04 8.98E−02 212094_at PEG10 chr7q21 −1.04 4.34E−02 204419_x_at HBG1 /// chr11p15.5 −1.03 1.34E−02 HBG2 204035_at SCG2 chr2q35-q36 −1.02 4.82E−02 212604_at MRPS31 chr13q14.11 −1.02 9.38E−03 216073_at ANKRD34C chr15q25.1 −1.02 5.36E−03 205399_at DCLK1 chr13q13 −1.02 3.87E−02 208002_s_at ACOT7 chr1p36.31-p36.11 −1.02 3.83E−02 221509_at DENR chr12q24.31 −1.01 2.80E−02 212992_at AHNAK2 chr14q32.33 −1.01 7.82E−03 204424_s_at LMO3 chr12p12.3 −1.01 5.72E−02 209569_x_at D4S234E chr4p16.3 −1.01 1.71E−02 205795_at NRXN3 chr14q31 −1.00 1.74E−02 204814_at CADPS chr3p14.2 −1.00 1.61E−02 209728_at HLA-DRB4 chr6p21.3 1.04 7.99E−03 221123_x_at ZNF395 chr8p21.1 1.04 4.57E−03 213089_at LOC100272216 — 1.06 1.58E−02 219728_at MYOT chr5q31 1.06 1.37E−02 207907_at TNFSF14 chr19p13.3 1.07 2.96E−04 214799_at NFASC chr1q32.1 1.08 1.13E−02 221755_at EHBP1L1 chr11q13.1 1.08 3.64E−04 212177_at SFRS18 chr6q16.3 1.09 1.24E−02 222299_x_at — — 1.10 4.73E−04 213164_at SLC5A3 chr21q22.12 1.11 2.56E−02 207142_at KCNJ3 chr2q24.1 1.12 3.12E−04 215071_s_at HIST1H2AC chr6p21.3 1.13 2.01E−02 209230_s_at NUPR1 chr16p11.2 1.14 5.37E−02 215555_at — — 1.14 8.23E−04 218566_s_at CHORDC1 chr11q14.3 1.17 2.78E−02 213716_s_at SECTM1 chr17q25 1.18 9.84E−04 220924_s_at SLC38A2 chr12q 1.19 6.37E−02 209309_at AZGP1 chr7q22.1 1.22 1.64E−02 201841_s_at HSPB1 chr7q11.23 1.22 8.98E−02 214682_at LOC399491 chr16p13.1 1.24 2.10E−03 218041_x_at SLC38A2 chr12q 1.24 7.07E−02 208513_at FOXB1 chr15q21-q26 1.36 3.74E−04 209339_at SIAH2 chr3q25 1.40 1.67E−03 215352_at GIMAP5 chr7q36.1 1.46 9.74E−05 209015_s_at DNAJB6 chr7q36.3 1.51 1.36E−02 200800_s_at HSPA1A /// chr6p21.3 1.56 1.29E−01 HSPA1B 213479_at NPTX2 chr7q21.3-q22.1 1.69 2.41E−02 208088_s_at CFHR5 chr1q22-q23 1.94 1.93E−06

indicates data missing or illegible when filed

SUPPLEMENTARY TABLE 7 This file contains the lists of genes differentially correlated with aSynL in PD vs Unaffected SN. Affymetrix Gene Correlation in Correlation Diff. Probeset Symbol Cytoband Control SN in PD SN Score 205311_at DDC chr7p12.2 0.998 0.333 −6.208 205110_s_at FGF13 chrXq26.3 0.990 −0.087 −5.587 207859_s_at CHRNB3 chr8p11.2 0.989 −0.047 −5.360 205445_at PRL chr6p22.2-p21.3 0.960 −0.521 −5.126 203997_at PTPN3 chr9q31 0.955 −0.478 −4.884 210454_s_at KCNJ6 chr21q22.1|21q22.13-q22.2 0.989 0.267 −4.736 216047_x_at SEZ6L chr22q12.1 0.978 −0.078 −4.736 209324_s_at RGS16 chr1q25-q31 0.961 −0.289 −4.582 218807_at VAV3 chr1p13.3 0.972 −0.083 −4.467 211894_x_at SEZ6L chr22q12.1 0.966 −0.088 −4.291 208092_s_at FAM49A chr2p24.3 0.877 −0.613 −4.209 207094_at IL8RA chr2q35 0.895 −0.527 −4.122 207522_s_at ATP2A3 chr17p13.3 0.961 −0.070 −4.113 209325_s_at RGS16 chr1q25-q31 0.928 −0.368 −4.109 207033_at GIF chr11q13 0.943 −0.255 −4.104 211562_s_at LMOD1 chr1q32 0.896 −0.519 −4.102 210547_x_at ICA1 chr7p22 0.818 −0.690 −4.051 218806_s_at VAV3 chr1p13.3 0.951 −0.158 −4.048 32502_at GDPD5 chr11q13.4-q13.5 0.892 −0.509 −4.040 206935_at PCDH8 chr13q14.3-q21.1 0.976 0.205 −4.031 207873_x_at SEZ6L chr22q12.1 0.946 −0.168 −3.971 201287_s_at SDC1 chr2p24.1 0.941 −0.202 −3.952 207195_at CNTN6 chr3p26-p25 0.877 −0.525 −3.948 221576_at GDF15 chr19p13.11 0.793 −0.696 −3.930 205696_s_at GFRA1 chr10q26.11 0.929 −0.264 −3.896 208291_s_at TH chr11p15.5 0.960 0.025 −3.891 219895_at FAM70A chrXq24 0.981 0.417 −3.832 212801_at CIT chr12q24 0.902 −0.384 −3.825 219772_s_at SMPX chrXp22.1 0.942 −0.125 −3.818 216086_at SV2C chr5q13.3 0.961 0.085 −3.808 205944_s_at CLTCL1 chr22q11.2|22q11.21 0.868 −0.498 −3.792 214811_at RIMBP2 chr12q24.33 0.940 −0.128 −3.788 220256_s_at OXCT2 chr1p34 0.945 −0.083 −3.784 213832_at KCND3 chr1p13.3 0.972 0.268 −3.750 220539_at C10orf92 chr10q26.3 0.882 −0.424 −3.721 203282_at GBE1 chr3p12.3 0.979 0.408 −3.709 219073_s_at OSBPL10 chr3p22.3 0.962 0.143 −3.705 219093_at PID1 chr2q36.3 0.941 −0.079 −3.697 218208_at

OC100131178 /// chr18q23 0.890 −0.379 −3.689 PQL

205857_at SLC18A2 chr10q25 0.980 0.439 −3.687 218631_at AVPI1 chr10q24.2 0.903 −0.319 −3.684 212316_at NUP210 chr3p25.1 0.923 −0.204 −3.677 213424_at KIAA0895 chr7p14.2 0.967 0.230 −3.673 205825_at PCSK1 chr5q15-q21 0.890 −0.362 −3.648 209530_at CACNB3 chr12q13 0.962 0.177 −3.642 215566_x_at LYPLA2 chr1p36.12-p35.1 0.962 0.181 −3.637 203680_at PRKAR2B chr7q22 0.969 0.288 −3.619 201410_at PLEKHB2 chr2q21.1 0.964 0.213 −3.617 204337_at RGS4 chr1q23.3 0.956 0.109 −3.616 221957_at PDK3 chrXp22.11 0.901 −0.288 −3.596 209981_at CSDC2 chr22q13.2-q13.31 0.865 −0.426 −3.586 215217_at — — 0.884 −0.353 −3.575 215153_at NOS1AP chr1q23.3 0.812 −0.557 −3.572 220559_at EN1 chr2q13-q21 0.969 0.300 −3.565 204556_s_at DZIP1 chr13q32.1 0.964 0.234 −3.562 215771_x_at RET chr10q11.2 0.972 0.366 −3.515 216548_x_at HMGB3L1 chr20q11.22 0.887 −0.315 −3.511 204269_at PIM2 chrXp11.23 0.941 0.019 −3.493 220762_s_at GNB1L chr22q11.2 0.839 −0.463 −3.479 211546_x_at SNCA chr4q21 0.951 0.139 −3.457 214156_at MYRIP chr3p22.1 0.961 0.257 −3.445 221344_at OR12D2 chr6p22.2-p21.31 0.888 −0.279 −3.439 214347_s_at DDC chr7p12.2 0.909 −0.168 −3.427 201286_at SDC1 chr2p24.1 0.940 0.050 −3.421 202681_at USP4 chr3p21.3 0.957 0.224 −3.404 222113_s_at EPS15L1 chr19p13.11 0.816 −0.488 −3.398 211173_at CCKAR chr4p15.1-p15.2 0.913 −0.126 −3.383 204261_s_at PSEN2 chr1q31-q42 0.931 −0.004 −3.383 205195_at AP1S1 chr7q22.1 0.852 −0.383 −3.381 210448_s_at P2RX5 chr17p13.3 0.914 −0.107 −3.366 213150_at HOXA10 chr7p15-p14 0.868 −0.312 −3.336 204105_s_at NRCAM chr7q31.1-q31.2 0.868 −0.300 −3.313 207167_at IGSF2 chr1p13 0.680 −0.667 −3.312 203823_at RGS3 chr9q32 0.822 −0.436 −3.301 202141_s_at COPS8 chr2q37.3 0.883 −0.233 −3.296 213938_at ERC2 chr3p14.3 0.957 0.286 −3.279 203999_at SYT1 chr12cen-q21 0.932 0.060 −3.272 217442_at LOC100131825 chr1q23.2 0.771 −0.529 −3.265 210286_s_at SLC4A7 chr3p22 0.652 −0.682 −3.263 211323_s_at ITPR1 chr3p26-p25 0.942 0.160 −3.238 221273_s_at RNF208 chr9q34.3 0.937 0.119 −3.233 218404_at SNX10 chr7p15.2 0.907 −0.080 −3.229 204604_at PFTK1 chr7q21-q22 0.939 0.137 −3.222 204059_s_at ME1 chr6q12 0.912 −0.048 −3.212 219203_at FAM158A chr14q11.2 0.888 −0.161 −3.191 212446_s_at LASS6 chr2q24.3 0.954 0.293 −3.185 204339_s_at RGS4 chr1q23.3 0.921 0.024 −3.181 203413_at NELL2 chr12q13.11-q13.12 0.896 −0.115 −3.174 210989_at LAMA4 chr6q21 0.700 −0.602 −3.166 216376_x_at — — 0.862 −0.254 −3.163 209947_at UBAP2L chr1q21.3 0.836 −0.334 −3.149 216944_s_at ITPR1 chr3p26-p25 0.943 0.208 −3.145 220904_at C6orf208 chr6q27 0.620 −0.679 −3.144 206456_at GABRA5 chr15q11.2-q12 0.867 −0.226 −3.142 209560_s_at DLK1 chr14q32 0.936 0.152 −3.140 203710_at ITPR1 chr3p26-p25 0.944 0.222 −3.134 211624_s_at DRD2 chr11q23 0.841 −0.310 −3.131 213476_x_at TUBB3 chr16q24.3 0.846 −0.293 −3.128 204224_s_at GCH1 chr14q22.1-q22.2 0.965 0.444 −3.123 210331_at HECW1 chr7p14.1-p13 0.821 −0.363 −3.120 207937_x_at FGFR1 chr8p11.2-p11.1 0.895 −0.092 −3.119 209783_at DBP chr19q13.3 0.839 −0.312 −3.118 211421_s_at RET chr10q11.2 0.966 0.454 −3.114 203439_s_at STC2 chr5q35.2 0.813 −0.379 −3.109 220721_at ZNF614 chr19q13.33 0.760 −0.492 −3.108 213726_x_at TUBB2C chr9q34 0.836 −0.316 −3.107 206950_at SCN9A chr2q24 0.823 −0.352 −3.106 205318_at KIF5A chr12q13.13 0.906 −0.026 −3.099 208463_at GABRA4 chr4p12 0.809 −0.384 −3.098 202606_s_at TLK1 chr2q31.1 0.865 −0.214 −3.096 209985_s_at ASCL1 chr12q23.2 0.601 −0.680 −3.086 204491_at PDE4D chr5q12 0.890 −0.098 −3.085 55065_at MARK4 chr19q13.3 0.879 −0.143 −3.073 208016_s_at AGTR1 chr3q21-q25 0.759 −0.477 −3.067 213609_s_at SEZ6L chr22q12.1 0.905 −0.010 −3.062 221844_x_at SPCS3 chr4q34.2 0.950 0.308 −3.058 216391_s_at KLHL1 chr13q21 0.820 −0.335 −3.052 219282_s_at TRPV2 chr17p11.2 0.915 0.053 −3.046 212992_at AHNAK2 chr14q32.33 0.876 −0.143 −3.046 200064_at HSP90AB1 chr6p12 0.880 −0.127 −3.045 203354_s_at PSD3 chr8pter-p23.3 0.911 0.030 −3.044 216256_at GRM8 chr7q31.3-q32.1 0.803 −0.376 −3.043 211909_x_at PTGER3 chr1p31.2 0.860 −0.201 −3.033 212653_s_at EHBP1 chr2p15 0.938 0.225 −3.022 211252_x_at PTCRA chr6p21.3 0.818 −0.328 −3.021 205835_s_at YTHDC2 chr5q22.2 0.902 −0.009 −3.020 210380_s_at CACNA1G chr17q22 0.874 −0.139 −3.017 214434_at HSPA12A chr10q26.12 0.910 0.039 −3.017 202501_at MAPRE2 chr18q12.1 0.787 −0.399 −3.009 209683_at FAM49A chr2p24.3 0.761 −0.452 −3.009 213558_at PCLO chr7q11.23-q21.3 0.903 0.006 −3.008 211593_s_at MAST2 chr1p34.1 0.943 0.275 −3.006 212590_at RRAS2 chr11p15.2 0.923 0.125 −3.001 213920_at CUX2 chr12q24.11-q24.12 0.784 −0.401 −3.000 218018_at PDXK chr21q22.3 0.867 −0.153 −2.988 204175_at ZNF593 chr1p36.11 0.905 0.031 −2.978 205632_s_at PIP5K1B chr9q13 0.962 0.470 −2.975 200650_s_at LDHA chr11p15.4 0.901 0.007 −2.974 203458_at SPR chr2p14-p12 0.957 0.416 −2.966 200870_at STRAP chr12p12.3 0.900 0.014 −2.960 214121_x_at PDLIM7 chr5q35.3 0.881 −0.078 −2.954 213902_at ASAH1 chr8p22-p21.3 0.872 −0.114 −2.953 205390_s_at ANK1 chr8p11.1 0.947 0.330 −2.953 206941_x_at SEMA3E chr7q21.11 0.788 −0.369 −2.948 216215_s_at RBM9 chr22q13.1 0.924 0.159 −2.948 221406_s_at C6orf26 /// chr6p21.3 /// 0.736 −0.471 −2.946 MSH5 chr6p21.33 210008_s_at MRPS12 chr19q13.1-q13.2 0.819 −0.291 −2.946 212224_at ALDH1A1 chr9q21.13 0.937 0.253 −2.944 217128_s_at CAMK1G chr1q32-q41 0.822 −0.281 −2.942 202832_at GCC2 chr2q12.3 0.875 −0.096 −2.940 216253_s_at PARVB chr22q13.2-q13.33 0.792 −0.355 −2.936 206592_s_at AP3D1 chr19p13.3 0.909 0.076 −2.930 214217_at GRM5 chr11q14.2-q14.3 0.813 −0.299 −2.929 205551_at SV2B chr15q26.1 0.918 0.129 −2.928 209444_at RAP1GDS1 chr4q23-q25 0.856 −0.165 −2.927 208034_s_at PROZ chr13q34 0.801 −0.327 −2.919 212851_at DCUN1D4 chr4q12 0.777 −0.380 −2.914 215728_s_at ACOT7 chr1p36.31-p36.11 0.890 −0.011 −2.907 200622_x_at CALM3 chr19q13.2-q13.3 0.838 −0.212 −2.899 213601_at SLIT1 chr10q23.3-q24 0.941 0.308 −2.896 209237_s_at SLC23A2 chr20p13 0.721 −0.478 −2.895 212960_at TBC1D9 chr4q31.21 0.929 0.224 −2.883 202684_s_at RNMT chr18p11.22-p11.23 0.701 −0.501 −2.878 207501_s_at FGF12 chr3q28 0.896 0.031 −2.877 34408_at RTN2 chr19q13.32 0.910 0.108 −2.876 37950_at PREP chr6q22 0.894 0.026 −2.867 202042_at HARS chr5q31.3 0.885 −0.015 −2.867 205566_at ABHD2 chr15q26.1 0.828 −0.229 −2.867 206046_at ADAM23 chr2q33 0.866 −0.097 −2.864 204991_s_at NF2 chr22q12.2 0.794 −0.318 −2.862 209635_at AP1S1 chr7q22.1 0.689 −0.511 −2.858 220131_at FXYD7 chr19q13.12 0.794 −0.316 −2.853 211577_s_at IGF1 chr12q22-q23 0.876 −0.048 −2.849 205196_s_at AP1S1 chr7q22.1 0.570 −0.639 −2.846 206502_s_at INSM1 chr20p11.2 0.921 0.186 −2.844 211383_s_at WDR37 chr10p15.3 0.887 0.005 −2.843 202154_x_at TUBB3 chr16q24.3 0.831 −0.207 −2.838 206527_at ABAT chr16p13.2 0.790 −0.318 −2.836 208845_at VDAC3 chr8p11.2 0.905 0.100 −2.834 205348_s_at DYNC1I1 chr7q21.3-q22.1 0.919 0.184 −2.833 202722_s_at GFPT1 chr2p13 0.864 −0.086 −2.829 219365_s_at CAMKV chr3p21.31 0.796 −0.299 −2.829 207422_at ADAM20 chr14q24.1 0.706 −0.475 −2.827 201714_at TUBG1 chr17q21 0.803 −0.279 −2.825 216092_s_at SLC7A8 chr14q11.2 0.871 −0.056 −2.824 202759_s_at

 /// chr9q31-q33 0.825 −0.218 −2.823 PALM2 /// PALM2-

207582_at PIN1L chr1p31 0.888 0.020 −2.821 206732_at SLITRK3 chr3q26.1 0.794 −0.301 −2.821 214306_at OPA1 chr3q28-q29|3q28-q29 0.823 −0.221 −2.817 204977_at DDX10 chr11q22-q23 0.914 0.158 −2.816 121_at PAX8 chr2q12-q14 0.759 −0.377 −2.816 205747_at CBLN1 chr16q12.1 0.936 0.305 −2.811 37965_at PARVB chr22q13.2-q13.33 0.712 −0.458 −2.807 206746_at BFSP1 chr20p11.23-p12.1 0.778 −0.332 −2.804 212956_at TBC1D9 chr4q31.21 0.920 0.201 −2.804 202913_at ARHGEF11 chr1q21 0.924 0.226 −2.801 213273_at ODZ4 chr11q14.1 0.632 −0.563 −2.798 218613_at PSD3 chr8pter-p23.3 0.887 0.027 −2.798 212946_at KIAA0564 chr13q14.11 0.865 −0.066 −2.797 220449_at MGC5566 chr20q13.12 0.805 −0.261 −2.795 201870_at TOMM34 — 0.854 −0.106 −2.793 218189_s_at NANS chr9p24.1-p23 0.908 0.141 −2.788 218856_at TNFRSF21 chr6p21.1-p12.2 0.515 −0.667 −2.787 214848_at — — 0.855 −0.099 −2.786 206421_s_at SERPINB7 chr18q21.33 0.791 −0.292 −2.784 207591_s_at ARID1A chr1p35.3 0.691 −0.480 −2.782 206065_s_at DPYS chr8q22 0.837 −0.161 −2.782 212442_s_at LASS6 chr2q24.3 0.933 0.299 −2.779 215150_at YOD1 chr1q32.1 0.680 −0.494 −2.777 40284_at FOXA2 chr20p11 0.856 −0.090 −2.775 203890_s_at DAPK3 chr19p13.3 0.756 −0.364 −2.772 212255_s_at ATP2C1 chr3q22.1 0.787 −0.296 −2.771 204338_s_at RGS4 chr1q23.3 0.859 −0.078 −2.771 203456_at PRAF2 chrXp11.23 0.860 −0.073 −2.771 219302_s_at CNTNAP2 chr7q35-q36 0.899 0.101 −2.770 204035_at SCG2 chr2q35-q36 0.847 −0.120 −2.770 219916_s_at RNF39 chr6p21.3 0.688 −0.480 −2.768 210652_s_at TTC39A chr1p32.3 0.904 0.124 −2.768 212728_at DLG3 chrXq13.1 0.846 −0.123 −2.767 215124_at ZNF550 chr19q13.43 0.627 −0.557 −2.766 205357_s_at AGTR1 chr3q21-q25 0.939 0.347 −2.763 207349_s_at UCP3 chr11q13 0.833 −0.165 −2.763 213808_at — — 0.864 −0.053 −2.761 209992_at PFKFB2 chr1q31 0.795 −0.267 −2.754 213059_at CREB3L1 chr11p11.2 0.606 −0.576 −2.754 216475_at — — 0.854 −0.089 −2.754 209453_at SLC9A1 chr1p36.1-p35 0.818 −0.205 −2.751 200078_s_at ATP6V0B chr1p32.3 0.880 0.018 −2.750 207827_x_at SNCA chr4q21 0.936 0.332 −2.749 203389_at KIF3C chr2p23 0.933 0.315 −2.745 212475_at AVL9 chr7p14.3 0.895 0.093 −2.743 219032_x_at OPN3 chr1q43 0.816 −0.207 −2.742 221560_at MARK4 chr19q13.3 0.753 −0.357 −2.740 212157_at SDC2 chr8q22-q23 0.947 0.425 −2.739 206679_at APBA1 chr9q13-q21.1 0.637 −0.535 −2.738 217162_at — — 0.709 −0.433 −2.731 204365_s_at REEP1 chr2p11.2 0.923 0.253 −2.730 213330_s_at STIP1 chr11q13 0.875 0.005 −2.730 207804_s_at FCN2 chr9q34.3 0.790 −0.267 −2.726 215014_at KCND3 chr1p13.3 0.927 0.282 −2.725 204586_at BSN chr3p21.31 0.893 0.094 −2.724 215097_at CAPZB chr1p36.1 0.898 0.115 −2.724 209935_at ATP2C1 chr3q22.1 0.753 −0.350 −2.724 213901_x_at RBM9 chr22q13.1 0.888 0.068 −2.722 221509_at DENR chr12q24.31 0.926 0.278 −2.721 213870_at COL11A2 chr6p21.3 0.770 −0.310 −2.717 217979_at TSPAN13 chr7p21.1 0.894 0.103 −2.715 206815_at SPAG8 chr9p13.3 0.746 −0.359 −2.714 206869_at CHAD chr17q21.33 0.513 −0.648 −2.712 207096_at SAA4 chr11p15.1-p14 0.738 −0.373 −2.709 219270_at CHAC1 chr15q15.1 0.842 −0.108 −2.706 204590_x_at VPS33A chr12q24.31 0.810 −0.204 −2.705 205011_at VWA5A chr11q23 0.920 0.248 −2.703 207521_s_at ATP2A3 chr17p13.3 0.812 −0.197 −2.702 34726_at CACNB3 chr12q13 0.930 0.311 −2.701 219736_at TRIM36 chr5q22.3 0.805 −0.217 −2.700 221269_s_at SH3BGRL3 chr1p35-p34.3 0.877 0.030 −2.699 206104_at ISL1 chr5q11.2 0.720 −0.401 −2.699 204730_at RIMS3 chr1pter-p22.2 0.786 −0.263 −2.696 208977_x_at TUBB2C chr9q34 0.789 −0.257 −2.695 216805_at — — 0.616 −0.545 −2.694 204574_s_at MMP19 chr12q14 0.757 −0.327 −2.693 222255_at PRX chr19q13.13-q13.2 0.698 −0.434 −2.691 201439_at GBF1 chr10q24 0.911 0.201 −2.689 216963_s_at GAP43 chr3q13.1-q13.2 0.885 0.076 −2.681 213198_at ACVR1B chr12q13 0.870 0.010 −2.681 212383_at ATP6V0A1 chr17q21 0.825 −0.149 −2.679 216967_at GAP43 chr3q13.1-q13.2 0.862 −0.020 −2.678 205879_x_at RET chr10q11.2 0.931 0.331 −2.676 205241_at SCO2 chr22q13.33 0.945 0.431 −2.676 204813_at MAPK10 chr4q22.1-q23 0.886 0.084 −2.675 218956_s_at PTCD1 chr7q22.1 0.903 0.166 −2.674 220482_s_at SERGEF chr11p14.3 0.915 0.235 −2.673 216533_at PCCA chr13q32 0.856 −0.040 −2.672 212055_at C18orf10 chr18q12.2 0.899 0.151 −2.668 212820_at DMXL2 chr15q21.2 0.876 0.043 −2.668 212695_at CRY2 chr11p11.2 0.845 −0.078 −2.665 217120_s_at MED14 chrXp11.4-p11.2 0.661 −0.477 −2.661 204816_s_at DHX34 chr19q13.3 0.836 −0.106 −2.661 202539_s_at HMGCR chr5q13.3-q14 0.874 0.037 −2.657 214874_at PKP4 chr2q23-q31 0.750 −0.326 −2.656 220173_at C14orf45 chr14q24.3 0.871 0.027 −2.655 214359_s_at HSP90AB1 chr6p12 0.791 −0.231 −2.652 203476_at TPBG chr6q14-q15 0.928 0.326 −2.651 212048_s_at YARS chr1p35.1 0.820 −0.149 −2.649 34221_at HMGXB3 chr5q33.1 0.793 −0.223 −2.648 214452_at BCAT1 chr12p12.1 0.778 −0.260 −2.648 217512_at KNG1 chr3q27 0.715 −0.388 −2.647 205095_s_at ATP6V0A1 chr17q21 0.752 −0.317 −2.646 219338_s_at LRRC49 chr15q23 0.857 −0.023 −2.645 210153_s_at ME2 chr6p25-p24|18q21 0.826 −0.129 −2.645 202263_at CYB5R1 chr1p36.13-q41 0.910 0.220 −2.644 207135_at HTR2A chr13q14-q21 0.810 −0.176 −2.644 221633_at NCAPH2 chr22q13.33 0.592 −0.554 −2.643 200734_s_at ARF3 chr12q13 0.900 0.168 −2.643 221533_at FAM162A chr3q21.1 0.740 −0.339 −2.638 202801_at PRKACA chr19p13.1 0.829 −0.117 −2.637 206481_s_at LDB2 chr4p16 0.781 −0.248 −2.636 203266_s_at MAP2K4 chr17p11.2 0.912 0.236 −2.636 216360_x_at RRP12 chr10q24.1 0.755 −0.305 −2.636 208693_s_at GARS chr7p15 0.812 −0.166 −2.635 206233_at B4GALT6 chr18q11 0.884 0.095 −2.632 210650_s_at PCLO chr7q11.23-q21.3 0.834 −0.096 −2.632 222234_s_at DBNDD1 chr16q24.3 0.839 −0.080 −2.631 209236_at SLC23A2 chr20p13 0.819 −0.142 −2.630 220201_at RC3H2 chr9q34 0.782 −0.243 −2.630 202142_at COPS8 chr2q37.3 0.805 −0.182 −2.628 204744_s_at IARS chr9q21 0.858 −0.011 −2.627 52837_at KIAA1644 — 0.735 −0.342 −2.625 204814_at CADPS chr3p14.2 0.905 0.201 −2.624 212213_x_at OPA1 chr3q28-q29|3q28-q29 0.838 −0.080 −2.621 204217_s_at RTN2 chr19q13.32 0.872 0.049 −2.619 218704_at RNF43 chr17q22 0.892 0.142 −2.615 214581_x_at TNFRSF21 chr6p21.1-p12.2 0.584 −0.553 −2.614 212104_s_at RBM9 chr22q13.1 0.902 0.191 −2.614 209599_s_at PRUNE chr1q21 0.645 −0.480 −2.613 204722_at SCN3B chr11q23.3 0.863 0.017 −2.612 216400_at GBA /// GBAP chr1q21 0.743 −0.318 −2.608 40255_at DDX28 chr16q22.1 0.734 −0.337 −2.607 206440_at LIN7A chr12q21 0.824 −0.116 −2.606 221750_at HMGCS1 chr5p14-p13 0.838 −0.069 −2.604 203017_s_at SSX2IP chr1p22.3 0.873 0.063 −2.599 217930_s_at TOLLIP chr11p15.5 0.787 −0.214 −2.597 202752_x_at SLC7A8 chr14q11.2 0.839 −0.063 −2.592 201500_s_at PPP1R11 chr6p21.3 0.848 −0.029 −2.592 211892_s_at PTGIS chr20q13.13 0.501 −0.622 −2.591 202872_at ATP6V1C1 chr8q22.3 0.853 −0.008 −2.586 216932_at — — 0.799 −0.176 −2.582 209923_s_at BRAP chr12q24 0.824 −0.103 −2.580 216444_at — — 0.579 −0.546 −2.580 205406_s_at SPA17 chr11q24.2 0.812 −0.136 −2.576 222206_s_at NCLN chr19p13.3 0.774 −0.236 −2.575 212242_at TUBA4A chr2q35 0.839 −0.052 −2.573 217319_x_at CYP4A22 chr1p33 0.788 −0.202 −2.573 202648_at — — 0.754 −0.279 −2.572 208824_x_at PCTK1 chrXp11.3-p11.23 0.749 −0.289 −2.571 220627_at CST8 chr20p11.21 0.791 −0.191 −2.570 214673_s_at HUWE1 chrXp11.22 0.891 0.158 −2.567 203826_s_at PITPNM1 chr11q13 0.841 −0.042 −2.563 212101_at KPNA6 chr1p35.1-p34.3 0.811 −0.134 −2.563 201050_at PLD3 chr19q13.2 0.840 −0.039 −2.555 203067_at PDHX chr11p13 0.892 0.169 −2.555 218662_s_at NCAPG chr4p15.33 0.973 0.706 −2.554 215169_at SLC35E2 chr1p36.33 0.726 −0.328 −2.554 219117_s_at FKBP11 chr12q13.12 0.928 0.367 −2.554 215492_x_at PTCRA chr6p21.3 0.837 −0.051 −2.554 202651_at LPGAT1 chr1q32 0.780 −0.211 −2.552 206573_at KCNQ3 chr8q24 0.589 −0.525 −2.552 208899_x_at ATP6V1D chr14q23-q24.2 0.828 −0.076 −2.552 202874_s_at ATP6V1C1 chr8q22.3 0.855 0.015 −2.551 220136_s_at CRYBA2 chr2q34-q36 0.837 −0.047 −2.549 204948_s_at FST chr5q11.2 0.543 −0.571 −2.546 214436_at FBXL2 chr3p22.3 0.869 0.071 −2.545 206078_at KALRN chr3q21.1-q21.2 0.629 −0.475 −2.544 217908_s_at IQWD1 chr1q24.2 0.891 0.170 −2.544 212607_at AKT3 chr1q43-q44 0.798 −0.161 −2.544 208017_s_at MCF2 chrXq27 0.808 −0.134 −2.544 203030_s_at PTPRN2 chr7q36 0.851 0.008 −2.540 204974_at RAB3A chr19p13.2 0.868 0.071 −2.538 215894_at PTGDR chr14q22.1 0.721 −0.330 −2.537 213308_at SHANK2 chr11q13.3 0.842 −0.024 −2.536 214096_s_at SHMT2 chr12q12-q14 0.890 0.169 −2.536 211714_x_at TUBB chr6p21.33 0.767 −0.235 −2.536 207658_s_at FOXG1 chr14q13 0.612 −0.492 −2.535 222230_s_at ACTR10 chr14q23.1 0.861 0.046 −2.534 222005_s_at GNG3 chr11p11 0.873 0.095 −2.534 213319_s_at CSDA chr12p13.1 0.675 −0.405 −2.532 208872_s_at REEP5 chr5q22-q23 0.808 −0.127 −2.530 200945_s_at SEC31A chr4q21.22 0.854 0.022 −2.529 201660_at ACSL3 chr2q34-q35 0.804 −0.134 −2.521 214969_at MAP3K9 chr14q24.3-q31 0.862 0.058 −2.518 209926_at LOC729991 chr19p13.11 0.685 −0.383 −2.517 213469_at PGAP1 chr2q33.1 0.778 −0.198 −2.516 206721_at C1orf114 chr1q24 0.907 0.264 −2.515 218817_at SPCS3 chr4q34.2 0.881 0.136 −2.515 219414_at CLSTN2 chr3q23-q24 0.761 −0.238 −2.515 215764_x_at AP2A2 chr11p15.5 0.813 −0.105 −2.512 209877_at SNCG chr10q23.2-q23.3 0.874 0.110 −2.510 216073_at ANKRD34C chr15q25.1 0.872 0.103 −2.509 209186_at ATP2A2 chr12q23-q24.1 0.722 −0.315 −2.506 214445_at ELL2 chr5q15 0.595 −0.501 −2.503 209011_at TRIO chr5p15.2 0.882 0.148 −2.502 205268_s_at ADD2 chr2p14-p13 0.879 0.137 −2.501 211712_s_at ANXA9 chr1q21 0.770 −0.210 −2.501 216076_at L3MBTL chr20q13.12 0.781 −0.185 −2.501 204165_at WASF1 chr6q21-q22 0.807 −0.116 −2.499 204795_at PRR3 chr6p21.33 0.664 −0.407 −2.496 219939_s_at CSDE1 chr1p22 0.922 0.354 −2.496 209026_x_at TUBB chr6p21.33 0.762 −0.226 −2.496 220486_x_at

C100130886 /// chrXq22.3 0.921 0.350 −2.496 TMEM

41047_at C9orf16 chr9q34.1 0.881 0.147 −2.496 218633_x_at ABHD10 chr3q13.2 0.830 −0.044 −2.495 1487_at ESRRA chr11q13 0.837 −0.021 −2.495 203841_x_at MAPRE3 chr2p23.3-p23.1 0.863 0.076 −2.494 201433_s_at PTDSS1 chr8q22 0.921 0.349 −2.494 201527_at ATP6V1F chr7q32 0.857 0.051 −2.493 202921_s_at ANK2 chr4q25-q27 0.819 −0.075 −2.493 209857_s_at SPHK2 chr19q13.2 0.824 −0.059 −2.492 206537_at XIAP chrXq25 0.806 −0.109 −2.485 201269_s_at NUDCD3 chr7p13-p12 0.861 0.074 −2.480 221069_s_at CCDC44 chr17q23.3 0.828 −0.042 −2.479 204743_at TAGLN3 chr3q13.2 0.886 0.176 −2.478 204869_at PCSK2 chr20p11.2 0.835 −0.017 −2.478 209556_at NCDN chr1p34.3 0.791 −0.146 −2.477 222064_s_at AARSD1 chr17q21.31 0.875 0.129 −2.476 219557_s_at NRIP3 chr11p15.3 0.842 0.009 −2.473 208316_s_at OCRL chrXq25-q26.1 0.843 0.011 −2.473 212853_at DCUN1D4 chr4q12 0.691 −0.353 −2.470 205636_at SH3GL3 chr15q24 0.647 −0.420 −2.469 204837_at MTMR9 chr8p23-p22 0.759 −0.220 −2.466 205549_at PCP4 chr21q22.2 0.746 −0.246 −2.464 210191_s_at PHTF1 chr1p13 0.857 0.066 −2.463 217098_s_at ZSCAN12 chr6p22.2-p21.3 0.699 −0.335 −2.461 218884_s_at GUF1 chr4p13 0.724 −0.291 −2.461 220117_at ZNF385D chr3p24.3 0.843 0.019 −2.457 207869_s_at CACNA1G chr17q22 0.782 −0.158 −2.452 205376_at INPP4B chr4q31.21 0.805 −0.098 −2.450 205047_s_at ASNS chr7q21.3 0.792 −0.132 −2.450 220942_x_at FAM162A chr3q21.1 0.758 −0.214 −2.449 212214_at OPA1 chr3q28- 0.805 −0.097 −2.449 q29|3q28-q29 219928_s_at CABYR chr18q11.2 0.862 0.091 −2.447 202043_s_at SMS chrXp22.1 0.866 0.108 −2.446 221901_at KIAA1644 — 0.775 −0.169 −2.439 212987_at FBXO9 chr6p12.3-p11.2 0.867 0.118 −2.438 201609_x_at ICMT chr1p36.21 0.856 0.074 −2.437 219572_at CADPS2 chr7q31.3 0.963 0.651 −2.437 208002_s_at ACOT7 chr1p36.31-p36.11 0.872 0.139 −2.437 206435_at B4GALNT1 chr12q13.3 0.838 0.013 −2.437 217393_x_at UBE2NL chrXq27.3 0.879 0.168 −2.436 219637_at ARMC9 chr2q37.1 0.799 −0.105 −2.435 208372_s_at LIMK1 chr7q11.23 0.676 −0.361 −2.431 209853_s_at PSME3 chr17q21 0.919 0.365 −2.431 221566_s_at NOL3 chr16q21-q23 0.783 −0.144 −2.430 204505_s_at EPB49 chr8p21.1 0.872 0.142 −2.429 214293_at 40432 chr4q21.1 0.761 −0.197 −2.428 218260_at DDA1 chr19p13.11 0.797 −0.107 −2.428 221211_s_at C21orf7 chr21q22.3 0.847 0.048 −2.425 200873_s_at CCT8 chr21q22.11 0.896 0.251 −2.424 208888_s_at NCOR2 chr12q24 0.740 −0.238 −2.419 205282_at LRP8 chr1p34 0.841 0.032 −2.419 211428_at SERPINA1 chr14q32.1 0.662 −0.377 −2.419 206339_at CARTPT chr5q13.2 0.823 −0.028 −2.417 221471_at SERINC3 chr20q13.1-q13.3 0.841 0.032 −2.416 216097_at — — 0.717 −0.282 −2.416 200720_s_at ACTR1A chr10q24.32 0.816 −0.047 −2.416 210527_x_at TUBA3C chr13q11 0.725 −0.268 −2.416 221792_at RAB6B chr3q22.1 0.855 0.083 −2.414 209397_at ME2 chr6p25-p24|18q21 0.811 −0.059 −2.412 206137_at RIMS2 chr8q22.3 0.803 −0.083 −2.410 202554_s_at GSTM3 chr1p13.3 0.833 0.009 −2.409 213036_x_at ATP2A3 chr17p13.3 0.830 −0.002 −2.409 204720_s_at DNAJC6 chr1pter-q31.3 0.875 0.166 −2.407 217231_s_at MAST1 chr19p13.2 0.802 −0.082 −2.407 205265_s_at SPEG chr2q35 0.807 −0.069 −2.407 209096_at UBE2V2 chr8q11.21 0.848 0.060 −2.406 210244_at CAMP chr3p21.3 0.606 −0.450 −2.406 213307_at SHANK2 chr11q13.3 0.832 0.007 −2.406 221727_at SUB1 chr5p13.3 0.870 0.143 −2.406 209410_s_at GRB10 chr7p12-p11.2 0.640 −0.404 −2.405 210065_s_at UPK1B chr3q13.3-q21 0.676 −0.350 −2.405 204870_s_at PCSK2 chr20p11.2 0.816 −0.042 −2.404 214844_s_at DOK5 chr20q13.2 0.855 0.087 −2.403 202572_s_at DLGAP4 chr20q11.23 0.807 −0.068 −2.402 206993_at ATP5S chr14q22.1 0.836 0.022 −2.402 218725_at SLC25A22 chr11p15.5 0.874 0.163 −2.402 219685_at TMEM35 chrXq22.1 0.887 0.220 −2.402 211971_s_at LRPPRC chr2p21 0.837 0.025 −2.401 214137_at PTPRJ chr11p11.2 0.670 −0.358 −2.400 205217_at TIMM8A chrXq22.1 0.774 −0.152 −2.399 206144_at MAGI1 chr3p14.1 0.899 0.275 −2.398 218359_at NRSN2 chr20p13 0.750 −0.206 −2.397 211566_x_at BRE chr2p23.2 0.756 −0.194 −2.397 200807_s_at HSPD1 chr2q33.1 0.807 −0.063 −2.396 214792_x_at VAMP2 chr17p13.1 0.793 −0.101 −2.396 200894_s_at FKBP4 chr12p13.33 0.838 0.032 −2.394 209345_s_at PI4K2A chr10q24 0.876 0.177 −2.394 219043_s_at LOC285359 /// chr2q11.2 /// 0.910 0.333 −2.392 PDCL3 chr3q12.3 215976_at — — 0.713 −0.279 −2.391 219856_at C1orf116 chr1q32.1 0.706 −0.292 −2.391 201822_at TIMM17A chr1q32.1 0.727 −0.251 −2.389 221066_at RXFP3 chr5p15.1-p14 0.867 0.141 −2.388 210868_s_at ELOVL6 chr4q25 0.720 −0.262 −2.384 200691_s_at HSPA9 chr5q31.1 0.818 −0.026 −2.383 207087_x_at ANK1 chr8p11.1 0.938 0.500 −2.380 215568_x_at

03956 ///

13.2 /// 0.882 0.206 −2.380 LYPLA2 /// chr1p36.12-p35.1 /// L

chr6

211123_at SLC5A5 chr19p13.2-p12 0.610 −0.435 −2.380 205937_at CGREF1 chr2p23.3 0.827 0.004 −2.379 221657_s_at ASB6 0.866 0.144 −2.375 210963_s_at GYG2 chrXp22.3 0.814 −0.032 −2.374 213132_s_at MCAT chr22q13.31 0.856 0.106 −2.374 211779_x_at AP2A2 chr11p15.5 0.835 0.032 −2.373 212361_s_at ATP2A2 chr12q23-q24.1 0.793 −0.092 −2.373 203527_s_at APC chr5q21-q22 0.882 0.213 −2.372 205810_s_at WASL chr7q31.3 0.637 −0.394 −2.370 207438_s_at SNUPN chr15q24.2 0.886 0.230 −2.369 222216_s_at MRPL17 chr11p15.5-p15.4 0.837 0.042 −2.367 208915_s_at GGA2 chr16p12 0.819 −0.013 −2.366 214772_at C11orf41 chr11p13 0.825 0.007 −2.363 211811_s_at PCDHA6 chr5q31 0.716 −0.260 −2.361 221959_at FAM110B chr8q12.1 0.823 0.001 −2.360 32541_at PPP3CC chr8p21.3 0.784 −0.107 −2.358 201174_s_at TERF2IP chr16q23.1 0.889 0.250 −2.358 40273_at SPHK2 chr19q13.2 0.809 −0.038 −2.357 217847_s_at THRAP3 chr1p34.3 0.762 −0.161 −2.357 201002_s_at

M189-UBE2V1 /// chr20q13.2 0.837 0.049 −2.356 UB

210924_at OLFM1 chr9q34.3 0.756 −0.173 −2.355 221324_at TAS2R1 chr5p15 0.703 −0.282 −2.355 206355_at GNAL chr18p11.22-p11.21 0.820 −0.005 −2.353 203998_s_at SYT1 chr12cen-q21 0.820 −0.005 −2.352 200825_s_at HYOU1 chr11q23.1-q23.3 0.753 −0.178 −2.352 207053_at SLC8A1 chr2p23-p22 0.756 −0.172 −2.352 204675_at SRD5A1 chr5p15 0.844 0.075 −2.352 212729_at DLG3 chrXq13.1 0.749 −0.188 −2.350 216277_at BUB1 chr2q14 0.545 −0.499 −2.350 208308_s_at GPI /// chr19q13.1 0.824 0.010 −2.349 LOC100133951 212971_at CARS chr11p15.5 0.831 0.031 −2.349 202504_at TRIM29 chr11q22-q23 0.594 −0.443 −2.349 220323_at CNTD2 chr19q13.2 0.650 −0.366 −2.348 202540_s_at HMGCR chr5q13.3-q14 0.856 0.119 −2.345 213222_at PLCB1 chr20p12 0.678 −0.321 −2.344 201760_s_at WSB2 chr12q24.23 0.897 0.293 −2.344 204540_at EEF1A2 chr20q13.3 0.845 0.083 −2.340 210525_x_at C14orf143 chr14q32.11 0.634 −0.385 −2.339 206610_s_at F11 chr4q35 0.761 −0.153 −2.336 213324_at SRC chr20q12-q13 0.850 0.103 −2.336 59437_at C9orf116 chr9q34.3 0.833 0.045 −2.333 206859_s_at PAEP chr9q34 0.750 −0.176 −2.331 212877_at KLC1 chr14q32.3 0.855 0.124 −2.331 202349_at TOR1A chr9q34 0.829 0.036 −2.328 214819_at IQSEC2 chrXp11.22 0.524 −0.513 −2.327 55093_at CSGLCA-T chr7q36.1 0.813 −0.012 −2.326 211249_at GPR68 chr14q31 0.687 −0.297 −2.324 205271_s_at CCRK chr9q22.1 0.804 −0.037 −2.324 204565_at ACOT13 chr6p22.2 0.839 0.071 −2.324 209973_at NFKBIL1 chr6p21.3 0.776 −0.111 −2.324 200815_s_at PAFAH1B1 chr17p13.3 0.747 −0.178 −2.322 33767_at NEFH chr22q12.2 0.849 0.107 −2.321 204256_at ELOVL6 chr4q25 0.698 −0.273 −2.319 211253_x_at PYY chr17q21.1 0.589 −0.437 −2.319 220878_at — — 0.678 −0.309 −2.317 219222_at RBKS chr2p23.3 0.885 0.251 −2.317 220260_at TBC1D19 chr4p15.2 0.828 0.037 −2.316 219486_at DUS2L chr16q22.1 0.746 −0.176 −2.314 209990_s_at GABBR2 chr9q22.1-q22.3 0.818 0.009 −2.314 213967_at RALYL chr8q21.2 0.907 0.352 −2.313 211433_x_at KIAA1539 chr9p13.3 0.635 −0.373 −2.312 212148_at PBX1 chr1q23 0.921 0.424 −2.312 201848_s_at BNIP3 chr10q26.3 0.775 −0.106 −2.311 202777_at SHOC2 chr10q25 0.899 0.317 −2.308 204466_s_at SNCA chr4q21 0.948 0.586 −2.308 205543_at HSPA4L chr4q28 0.840 0.084 −2.306 215458_s_at SMURF1 chr7q22.1 0.811 −0.007 −2.306 206836_at SLC6A3 chr5p15.3 0.914 0.389 −2.306 207239_s_at PCTK1 chrXp11.3-p11.23 0.671 −0.314 −2.306 210135_s_at SHOX2 chr3q25-q26.1 0.535 −0.493 −2.305 205839_s_at BZRAP1 chr17q22-q23 0.838 0.078 −2.302 220091_at SLC2A6 chr9q34 0.878 0.227 −2.302 202260_s_at STXBP1 chr9q34.1 0.845 0.100 −2.302 207000_s_at PPP3CC chr8p21.3 0.830 0.053 −2.301 217887_s_at EPS15 chr1p32 0.714 −0.236 −2.300 211622_s_at ARF3 chr12q13 0.880 0.237 −2.300 213997_at KIAA0574 chr15q12 0.790 −0.064 −2.299 211203_s_at CNTN1 chr12q11-q12 0.835 0.071 −2.298 218623_at HMP19 chr5q35.2 0.855 0.138 −2.297 203231_s_at ATXN1 chr6p23 0.752 −0.155 −2.296 208850_s_at THY1 chr11q22.3-q23 0.827 0.047 −2.295 214762_at ATP6V1G2 chr6p21.3 0.830 0.055 −2.295 212151_at PBX1 chr1q23 0.935 0.512 −2.295 214270_s_at MAPRE3 chr2p23.3-p23.1 0.845 0.105 −2.295 201411_s_at PLEKHB2 chr2q21.1 0.767 −0.119 −2.295 200640_at YWHAZ chr8q23.1 0.790 −0.060 −2.294 205822_s_at HMGCS1 chr5p14-p13 0.817 0.016 −2.293 217711_at TEK chr9p21 0.587 −0.428 −2.292 214077_x_at MEIS3P1 chr17p12 0.885 0.261 −2.292 209627_s_at OSBPL3 chr7p15 0.873 0.209 −2.292 204650_s_at APBB3 chr5q31 0.755 −0.145 −2.291 211167_s_at GCK chr7p15.3-p15.1 0.782 −0.079 −2.290 202912_at ADM chr11p15.4 0.760 −0.134 −2.290 207452_s_at CNTN5 chr11q21-q22.2 0.708 −0.243 −2.290 213550_s_at TMCO6 chr5q31.3 0.825 0.043 −2.289 208851_s_at THY1 chr11q22.3-q23 0.860 0.165 −2.286 201089_at ATP6V1B2 chr8p22-p21 0.842 0.099 −2.286 221371_at TNFSF18 chr1q23 0.809 −0.004 −2.286 219400_at CNTNAP1 chr17q21 0.861 0.169 −2.285 214272_at CYLD chr16q12.1 0.712 −0.231 −2.282 217574_at CDH8 chr16q22.1 0.763 −0.123 −2.282 201889_at FAM3C chr7q31 0.825 0.046 −2.282 217457_s_at RAP1GDS1 chr4q23-q25 0.769 −0.109 −2.282 208353_x_at ANK1 chr8p11.1 0.928 0.477 −2.282 65521_at UBE2D4 chr7p13 0.735 −0.185 −2.281 205691_at SYNGR3 chr16p13 0.861 0.169 −2.281 222132_s_at AGK chr7q34 0.844 0.110 −2.280 215407_s_at ASTN2 chr9q33.1 0.797 −0.036 −2.280 204723_at SCN3B chr11q23.3 0.847 0.123 −2.275 205257_s_at AMPH chr7p14-p13 0.865 0.188 −2.275 213374_x_at HIBCH chr2q32.2 0.865 0.188 −2.275 202517_at CRMP1 chr4p16.1-p15 0.775 −0.090 −2.274 209372_x_at TUBB2A /// chr6p25 0.673 −0.296 −2.273 TUBB2B 202854_at HPRT1 chrXq26.1 0.857 0.160 −2.273 206751_s_at PCYT1B chrXp22.11 0.748 −0.151 −2.272 200695_at PPP2R1A chr19q13.33 0.744 −0.159 −2.270 209029_at COPS7A chr12p13.31 0.782 −0.069 −2.270 202158_s_at CUGBP2 chr10p13 0.739 −0.170 −2.269 204527_at MYO5A chr15q21 0.811 0.010 −2.268 220105_at RTDR1 chr22q11.2 0.606 −0.394 −2.266 205638_at BAI3 chr6q12 0.839 0.100 −2.265 202582_s_at RANBP9 chr6p23 0.909 0.384 −2.265 209014_at MAGED1 chrXp11.23 0.836 0.090 −2.264 201266_at TXNRD1 chr12q23-q24.1 0.726 −0.194 −2.264 205827_at CCK chr3p22-p21.3 0.747 −0.150 −2.264 201972_at ATP6V1A chr3q13.2-q13.31 0.852 0.148 −2.262 212358_at CLIP3 chr19q13.12 0.792 −0.039 −2.261 205735_s_at AFF3 chr2q11.2-q12 0.736 −0.173 −2.261 218434_s_at AACS chr12q24.31 0.834 0.086 −2.256 212094_at PEG10 chr7q21 0.937 0.536 −2.256 209249_s_at GHITM chr10q23.1 0.830 0.075 −2.256 210628_x_at LTBP4 chr19q13.1-q13.2 0.584 −0.416 −2.254 218955_at BRF2 chr8p12 0.866 0.200 −2.254 206876_at SIM1 chr6q16.3-q21 0.661 −0.307 −2.254 221262_s_at SLC2A11 chr22q11.2 0.702 −0.236 −2.253 220479_at LOC29034 chr2q34 0.691 −0.256 −2.253 214079_at DHRS2 chr14q11.2 0.648 −0.327 −2.253 213617_s_at C18orf10 chr18q12.2 0.818 0.039 −2.252 205004_at NKRF chrXq24 0.789 −0.042 −2.251 208737_at ATP6V1G1 chr9q32 0.830 0.077 −2.249 206528_at TRPC6 chr11q21-q22 0.625 −0.359 −2.248 220841_s_at AHI1 chr6q23.3 0.748 −0.140 −2.248 204486_at — — 0.666 −0.296 −2.247 201453_x_at RHEB chr7q36 0.846 0.133 −2.246 218560_s_at JMJD4 chr1q42.13 0.735 −0.167 −2.246 212137_at LARP1 chr5q33.2 0.898 0.339 −2.246 201678_s_at C3orf37 chr3q21.3 0.887 0.291 −2.245 211609_x_at PSMD4 chr1q21.2 0.825 0.063 −2.244 202965_s_at CAPN6 chrXq23 0.618 −0.369 −2.244 211156_at CDKN2A chr9p21 0.764 −0.101 −2.243 212880_at WDR7 chr18q21.1-q22 0.825 0.067 −2.242 200982_s_at ANXA6 chr5q32-q34 0.788 −0.039 −2.241 205864_at SLC7A4 chr22q11.21 0.786 −0.045 −2.240 210966_x_at LARP1 chr5q33.2 0.855 0.169 −2.240 214164_x_at CA12 chr15q22 0.551 −0.450 −2.239 215167_at MED14 chrXp11.4-p11.2 0.646 −0.323 −2.236 211153_s_at TNFSF11 chr13q14 0.683 −0.263 −2.236 201849_at BNIP3 chr10q26.3 0.691 −0.248 −2.235 201557_at VAMP2 chr17p13.1 0.848 0.145 −2.234 213869_x_at THY1 chr11q22.3-q23 0.847 0.142 −2.234 212353_at SULF1 chr8q13.2-q13.3 0.652 −0.312 −2.231 221903_s_at CYLD chr16q12.1 0.757 −0.111 −2.230 216236_s_at SLC2A14 /// chr12p13.3 /// 0.807 0.018 −2.230 SLC2A3 chr12p13.31 207059_at PAX9 chr14q12-q13 0.732 −0.166 −2.230 213439_x_at RUNDC3A chr17q21.31 0.890 0.309 −2.229 212159_x_at AP2A2 chr11p15.5 0.847 0.147 −2.226 204117_at PREP chr6q22 0.768 −0.084 −2.226 209587_at PITX1 chr5q31 0.645 −0.320 −2.225 200863_s_at RAB11A chr15q21.3-q22.31 0.844 0.137 −2.225 214976_at RPL13 chr16q24.3|17p11.2 0.622 −0.354 −2.225 201313_at ENO2 chr12p13 0.809 0.027 −2.224 200740_s_at SUMO3 chr21q22.3 0.865 0.212 −2.224 203179_at GALT chr9p13 0.858 0.185 −2.223 204554_at PPP1R3D chr20q13.3 0.907 0.393 −2.223 210517_s_at AKAP12 chr6q24-q25 0.867 0.220 −2.222 206356_s_at GNAL chr18p11.22-p11.21 0.844 0.137 −2.222 218137_s_at SMAP1 chr6q13 0.833 0.101 −2.221 56829_at TRAPPC9 chr8q24.3 0.730 −0.165 −2.221 215634_at — — 0.828 0.085 −2.220 204146_at RAD51AP1 chr12p13.2-p13.1 0.809 0.029 −2.219 205359_at AKAP6 chr14q13.1 0.818 0.056 −2.219 217655_at LOC100127972 chr19q13.12 0.544 −0.450 −2.219 204412_s_at NEFH chr22q12.2 0.834 0.107 −2.216 209537_at EXTL2 chr1p21 0.853 0.170 −2.216 222021_x_at SDHALP1 chr3q29 0.768 −0.078 −2.215 221063_x_at RNF123 chr3p24.3 0.743 −0.136 −2.215 217785_s_at YKT6 chr7p15.1 0.735 −0.152 −2.214 207789_s_at DPP6 chr7q36.2 0.845 0.146 −2.214 203817_at GUCY1B3 chr4q31.3-q33 0.825 0.079 −2.214 205030_at FABP7 chr6q22-q23 0.918 0.447 −2.214 219350_s_at DIABLO chr12q24.31 0.800 0.008 −2.213 209720_s_at SERPINB3 chr18q21.3 0.665 −0.283 −2.212 216316_x_at GK /// chr4q32.1 /// 0.619 −0.352 −2.212 GK3P chrXp21.3 49077_at PPME1 chr11q13.4 0.836 0.116 −2.211 210510_s_at NRP1 chr10p12 0.549 −0.441 −2.208 217186_at ZNF259P chr6q21 0.776 −0.053 −2.206 217093_at RNASE1 chr14q11.2 0.821 0.072 −2.206 202196_s_at DKK3 chr11p15.2 0.827 0.090 −2.206 216938_x_at DRD2 chr11q23 0.798 0.005 −2.204 217606_at — — 0.817 0.060 −2.204 205773_at CPEB3 chr10q23.32 0.946 0.610 −2.203 204970_s_at MAFG chr17q25.3 0.738 −0.139 −2.203 39582_at CYLD chr16q12.1 0.779 −0.043 −2.201 203931_s_at MRPL12 chr17q25 0.797 0.005 −2.201 209772_s_at CD24 chr6q21 0.536 −0.452 −2.201 221029_s_at WNT5B chr12p13.3 0.605 −0.368 −2.200 222125_s_at P4HTM chr3p21.31 0.734 −0.147 −2.200 209206_at SEC22B chr1q21.1 0.703 −0.210 −2.200 205673_s_at ASB9 — 0.516 −0.474 −2.200 209211_at KLF5 chr13q22.1 0.842 0.142 −2.199 219060_at WDYHV1 chr8q24.13 0.744 −0.125 −2.199 206347_at PDK3 chrXp22.11 0.764 −0.079 −2.198 216477_at — — 0.772 −0.060 −2.198 204471_at GAP43 chr3q13.1-q13.2 0.828 0.098 −2.196 210465_s_at SNAPC3 chr9p22.3 0.736 −0.141 −2.195 214230_at CDC42 chr1p36.1 0.824 0.085 −2.194 203820_s_at IGF2BP3 chr7p11 0.722 −0.169 −2.194 218111_s_at CMAS chr12p12.1 0.867 0.234 −2.194 220538_at ADM2 chr22q13.33 0.640 −0.313 −2.193 206290_s_at RGS7 chr1q43|1q23.1 0.840 0.140 −2.190 218412_s_at GTF2IRD1 chr7q11.23 0.708 −0.194 −2.188 204513_s_at ELMO1 chr7p14.2 0.812 0.053 −2.188 206976_s_at HSPH1 chr13q12.3 0.724 −0.163 −2.187 200820_at PSMD8 chr19q13.2 0.802 0.025 −2.187 207594_s_at SYNJ1 chr21q22.2 0.788 −0.011 −2.185 204364_s_at REEP1 chr2p11.2 0.860 0.211 −2.184 207210_at GABRA3 chrXq28 0.753 −0.096 −2.183 204629_at PARVB chr22q13.2-q13.33 0.769 −0.060 −2.183 200822_x_at TPI1 chr12p13 0.749 −0.107 −2.182 205389_s_at ANK1 chr8p11.1 0.921 0.474 −2.182 221458_at HTR1F chr3p12 0.621 −0.336 −2.182 220896_at FBXL18 chr7p22.2 0.807 0.043 −2.182 204352_at TRAF5 chr1q32 0.669 −0.261 −2.180 218568_at AGK chr7q34 0.801 0.025 −2.179 205795_at NRXN3 chr14q31 0.849 0.175 −2.177 203538_at CAMLG chr5q23 0.899 0.374 −2.176 213486_at COPG2IT1 chr7q32 0.851 0.185 −2.176 201543_s_at SAR1A chr10q22.1 0.652 −0.287 −2.175 218482_at ENY2 chr8q23.1 0.833 0.125 −2.174 203895_at PLCB4 chr20p12 0.845 0.164 −2.173 208524_at GPR15 chr3q11.2-q13.1 0.551 −0.424 −2.173 215108_x_at TOX3 chr16q12.1 0.775 −0.040 −2.172 217004_s_at MCF2 chrXq27 0.758 −0.081 −2.172 205567_at CHST1 chr11p11.2-p11.1 0.767 −0.060 −2.172 207387_s_at GK chrXp21.3 0.697 −0.206 −2.171 201658_at ARL1 chr12q23.2 0.726 −0.151 −2.171 213011_s_at TPI1 chr12p13 0.737 −0.127 −2.171 202849_x_at GRK6 chr5q35 0.541 −0.435 −2.171 200641_s_at YWHAZ chr8q23.1 0.742 −0.116 −2.170 213433_at ARL3 chr10q23.3 0.765 −0.062 −2.169 212471_at AVL9 chr7p14.3 0.709 −0.183 −2.167 200639_s_at YWHAZ chr8q23.1 0.695 −0.209 −2.166 201415_at GSS chr20q11.2 0.805 0.044 −2.166 219100_at OBFC1 chr10q24.33 0.699 −0.202 −2.166 212372_at MYH10 chr17p13 0.812 0.064 −2.165 218456_at CAPRIN2 chr12p11 0.879 0.293 −2.164 203797_at VSNL1 chr2p24.3 0.815 0.075 −2.162 217305_s_at ADCY10 chr1q24 0.603 −0.353 −2.162 222261_at KIAA1609 chr16q24.1 0.519 −0.456 −2.161 205852_at CDK5R2 chr2q35 0.824 0.103 −2.161 218100_s_at IFT57 chr3q13.12 0.741 −0.113 −2.161 209384_at PROSC chr8p11.2 0.890 0.342 −2.160 208352_x_at ANK1 chr8p11.1 0.930 0.532 −2.158 220416_at ATP8B4 chr15q21.2 0.614 −0.336 −2.158 203159_at GLS chr2q32-q34 0.853 0.201 −2.157 214098_at KIAA1107 chr1p22.1 0.776 −0.029 −2.157 209755_at NMNAT2 chr1q25 0.864 0.241 −2.154 218737_at SBNO1 chr12q24.31 0.853 0.201 −2.154 203446_s_at OCRL chrXq25-q26.1 0.852 0.199 −2.153 215101_s_at CXCL5 chr4q12-q13 0.699 −0.195 −2.152 216623_x_at TOX3 chr16q12.1 0.777 −0.024 −2.150 219508_at GCNT3 chr15q21.3 0.679 −0.230 −2.150 213066_at RUSC2 chr9p13.3 0.749 −0.089 −2.150 208276_at — — 0.729 −0.134 −2.149 206812_at ADRB3 chr8p12-p11.2 0.752 −0.083 −2.148 205850_s_at GABRB3 chr15q11.2-q12 0.779 −0.018 −2.148 212497_at MAPK1IP1L chr14q22.3 0.545 −0.420 −2.148 218106_s_at MRPS10 chr6p21.1 0.826 0.116 −2.147 200638_s_at YWHAZ chr8q23.1 0.794 0.023 −2.147 208702_x_at APLP2 chr11q23-q25|11q24 0.807 0.060 −2.147 214745_at PLCH1 chr3q25.31 0.907 0.423 −2.147 212554_at CAP2 chr6p22.3 0.811 0.072 −2.146 211679_x_at GABBR2 chr9q22.1-q22.3 0.788 0.006 −2.145 214757_at PMS2L2 chr7q11-q22 0.750 −0.085 −2.144 201122_x_at EIF5A chr17p13-p12 0.635 −0.298 −2.144 35666_at SEMA3F chr3p21.3 0.630 −0.307 −2.144 211320_s_at PTPRU chr1p35.3-p35.1 0.728 −0.133 −2.144 206044_s_at BRAF chr7q34 0.799 0.039 −2.143 203410_at AP3M2 chr8p11.2 0.754 −0.076 −2.143 203368_at CRELD1 chr3p25.3 0.655 −0.266 −2.143 207184_at SLC6A13 chr12p13.3 0.531 −0.434 −2.142 221567_at NOL3 chr16q21-q23 0.835 0.144 −2.142 204375_at CLSTN3 chr12p13.31 0.849 0.194 −2.142 209859_at TRIM9 chr14q22.1 0.736 −0.115 −2.141 210616_s_at SEC31A chr4q21.22 0.692 −0.202 −2.139 204044_at QPRT chr16p11.2 0.829 0.130 −2.139 203172_at FXR2 chr17p13.1 0.848 0.192 −2.138 220615_s_at FAR2 chr12p11.22 0.776 −0.020 −2.138 221859_at SYT13 chr11p12-p11 0.755 −0.071 −2.137 212798_s_at ANKMY2 chr7p21 0.835 0.148 −2.137 212009_s_at STIP1 chr11q13 0.707 −0.171 −2.137 219591_at CEND1 chr11p15.5 0.818 0.097 −2.136 211207_s_at ACSL6 chr5q31 0.768 −0.038 −2.136 214803_at — — 0.725 −0.134 −2.135 218393_s_at SMU1 chr9p12 0.776 −0.018 −2.133 214999_s_at RAB11FIP3 chr16p13.3 0.790 0.020 −2.133 205792_at WISP2 chr20q12-q13.1 0.694 −0.194 −2.130 221393_at TAAR3 chr6q23-q24 0.780 −0.005 −2.130 205539_at AVIL chr12q14.1 0.691 −0.199 −2.129 201403_s_at MGST3 chr1q23 0.792 0.027 −2.129 210050_at TPI1 chr12p13 0.833 0.147 −2.128 212990_at SYNJ1 chr21q22.2 0.857 0.228 −2.128 216190_x_at ITGB1 chr10p11.2 0.707 −0.167 −2.127 206217_at EDA chrXq12-q13.1 0.656 −0.257 −2.127 211586_s_at

P2B2 /// chr3p25.3 0.730 −0.118 −2.124 LOC1001342

206031_s_at USP5 chr12p13 0.688 −0.201 −2.123 209991_x_at GABBR2 chr9q22.1-q22.3 0.768 −0.033 −2.122 213912_at FLJ41278 /// chr12q14.3 0.828 0.134 −2.121 TBC1D30 203157_s_at GLS chr2q32-q34 0.837 0.162 −2.121 204106_at TESK1 chr9p13 0.791 0.027 −2.120 211761_s_at CACYBP chr1q24-q25 0.864 0.256 −2.120 221048_x_at C17orf80 chr17q25.1 0.809 0.078 −2.119 209767_s_at GP1BB ///

11.21 /// 0.759 −0.052 −2.117 SEPT5 chr22q11.21- q11.23|22

222175_s_at MED15 chr22q11.2 0.659 −0.248 −2.117 212565_at STK38L chr12p11.23 0.860 0.245 −2.116 221345_at FFAR2 chr19q13.1 0.603 −0.333 −2.115 201523_x_at UBE2N chr12q22 0.787 0.020 −2.115 214607_at PAK3 chrXq22.3 0.783 0.009 −2.115 210305_at PDE4DIP chr1q12 0.742 −0.088 −2.112 204611_s_at PPP2R5B chr11q12-q13 0.804 0.067 −2.112 203773_x_at BLVRA chr7p14-cen 0.864 0.261 −2.112 201193_at IDH1 chr2q33.3 0.823 0.123 −2.112 217339_x_at CTAG1A /// chrXq28 0.557 −0.391 −2.111 CTAG1B 220830_at IMPG2 chr3q12.2-q12.3 0.726 −0.121 −2.110 216948_at — — 0.682 −0.204 −2.109 209658_at CDC16 chr13q34 0.752 −0.062 −2.108 220405_at

C100127998 /// chr8q11-q12 /// 0.813 0.097 −2.106 SNT

chr8q11.22 213531_s_at RAB3GAP1 chr2q21.3 0.872 0.293 −2.106 205204_at NMB chr15q22-qter 0.810 0.088 −2.105 215910_s_at FNDC3A chr13q14.2 0.523 −0.429 −2.105 218680_x_at HYPK chr15q15.3 0.843 0.189 −2.105 203158_s_at GLS chr2q32-q34 0.796 0.049 −2.105 212149_at EFR3A chr8q24.22 0.837 0.172 −2.104 39705_at SIN3B chr19p13.11 0.854 0.229 −2.104 215670_s_at SCAND2 chr15q25-q26 0.682 −0.203 −2.104 211985_s_at CALM1 chr14q24-q31 0.749 −0.067 −2.102 202836_s_at TXNL4A chr18q23 0.786 0.024 −2.102 200987_x_at PSME3 chr17q21 0.878 0.319 −2.101 219688_at BBS7 chr4q27 0.757 −0.047 −2.099 215785_s_at CYFIP2 chr5q33.3 0.754 −0.053 −2.099 213927_at MAP3K9 chr14q24.3-q31 0.833 0.160 −2.099 210143_at ANXA10 chr4q33 0.569 −0.371 −2.098 212333_at FAM98A chr2p22.3 0.765 −0.027 −2.098 204076_at ENTPD4 chr8p21.3 0.839 0.182 −2.098 208075_s_at CCL7 chr17q11.2-q12 0.653 −0.249 −2.097 212362_at ATP2A2 chr12q23-q24.1 0.600 −0.329 −2.095 214376_at — — 0.834 0.167 −2.094 207816_at LALBA chr12q13 0.537 −0.408 −2.093 205391_x_at ANK1 chr8p11.1 0.924 0.525 −2.092 221597_s_at TMEM208 chr16q22.1 0.827 0.144 −2.092 213875_x_at C6orf62 chr6p22.2 0.672 −0.215 −2.092 211195_s_at TP63 chr3q28 0.772 −0.006 −2.092 216913_s_at RRP12 chr10q24.1 0.712 −0.141 −2.092 202394_s_at ABCF3 chr3q27.1 0.814 0.106 −2.091 208709_s_at NRD1 chr1p32.2-p32.1 0.851 0.222 −2.091 201994_at MORF4L2 chrXq22 0.726 −0.110 −2.090 204480_s_at C9orf16 chr9q34.1 0.804 0.079 −2.089 203589_s_at TFDP2 chr3q23 0.806 0.084 −2.089 210976_s_at PFKM chr12q13.3 0.821 0.128 −2.087 214447_at ETS1 chr11q23.3 0.649 −0.251 −2.087 222088_s_at SLC2A14 /// chr12p13.3 /// 0.727 −0.106 −2.086 SLC2A3 chr12p13.31 216330_s_at POU6F1 chr12q13.13 0.869 0.292 −2.085 205556_at MSX2 chr5q34-q35 0.687 −0.185 −2.085 221181_at — — 0.631 −0.278 −2.084 216489_at TRPM3 chr9q21.11-q21.12 0.693 −0.173 −2.084 219275_at PDCD5 chr19q12-q13.1 0.820 0.129 −2.084 214268_s_at MTMR4 chr17q22-q23 0.829 0.155 −2.082 219901_at FGD6 chr12q22 0.680 −0.195 −2.081 221214_s_at NELF chr9q34.3 0.610 −0.308 −2.081 220910_at FRAS1 chr4q21.21 0.520 −0.422 −2.080 213406_at WSB1 chr17q11.1 0.647 −0.251 −2.080 202033_s_at RB1CC1 chr8q11 0.809 0.097 −2.079 202372_at RAB3GAP2 chr1q41 0.831 0.163 −2.079 206181_at SLAMF1 chr1q22-q23 0.541 −0.396 −2.078 214774_x_at TOX3 chr16q12.1 0.735 −0.087 −2.078 201381_x_at CACYBP chr1q24-q25 0.840 0.193 −2.077 213295_at CYLD chr16q12.1 0.797 0.066 −2.076 203029_s_at PTPRN2 chr7q36 0.796 0.062 −2.075 214975_s_at MTMR1 chrXq28 0.822 0.137 −2.075 207088_s_at SLC25A11 chr17p13.3 0.717 −0.121 −2.075 211925_s_at PLCB1 chr20p12 0.702 −0.151 −2.074 217755_at HN1 chr17q25.1 0.871 0.306 −2.073 202422_s_at ACSL4 chrXq22.3-q23 0.859 0.260 −2.072 221693_s_at MRPS18A chr6p21.3 0.668 −0.213 −2.072 214342_at ATXN7L1 chr7q22.2 0.568 −0.361 −2.071 214383_x_at KLHDC3 chr6p21.1 0.803 0.085 −2.070 201709_s_at NIPSNAP1 chr22q12.2 0.825 0.151 −2.069 201434_at TTC1 chr5q33.3 0.851 0.236 −2.068 202513_s_at PPP2R5D chr6p21.1 0.780 0.024 −2.068 214277_at COX11 chr17q22 0.785 0.040 −2.066 218550_s_at LRRC20 chr10q22.1 0.744 −0.060 −2.066 217129_at — — 0.606 −0.307 −2.066 203814_s_at NQO2 chr6pter-q12 0.783 0.034 −2.066 217310_s_at FOXJ3 chr1pter-q31.3 0.657 −0.228 −2.066 204945_at PTPRN chr2q35-q36.1 0.791 0.057 −2.064 219335_at ARMCX5 chrXq22.1-q22.3 0.733 −0.083 −2.063 221316_at C19orf15 chr19q13.1 0.651 −0.237 −2.062 203333_at KIFAP3 chr1q24.2 0.825 0.153 −2.062 212842_x_at

// chr2q12.3 /// 0.717 −0.116 −2.062 RGPD5 /// chr2q13 RGPD6 //

222286_at SNAPC3 chr9p22.3 0.886 0.370 −2.061 221912_s_at CCDC28B chr1p35.1 0.799 0.079 −2.059 200978_at MDH1 chr2p13.3 0.784 0.040 −2.059 200895_s_at FKBP4 chr12p13.33 0.754 −0.034 −2.058 210959_s_at SRD5A1 chr5p15 0.714 −0.120 −2.057 217356_s_at PGK1 chrXq13 0.755 −0.029 −2.055 207022_s_at LDHC chr11p15.5-p15.3 0.870 0.309 −2.055 203438_at STC2 chr5q35.2 0.670 −0.200 −2.055 201556_s_at VAMP2 chr17p13.1 0.782 0.037 −2.054 214095_at SHMT2 chr12q12-q14 0.708 −0.130 −2.053 204564_at PCGF3 chr4p16.3 0.880 0.348 −2.050 211347_at CDC14B chr9q22.33 0.729 −0.086 −2.049 215608_at — — 0.743 −0.053 −2.048 213683_at ACSL6 chr5q31 0.802 0.095 −2.047 217841_s_at PPME1 chr11q13.4 0.836 0.194 −2.047 203224_at RFK chr9q21.13 0.853 0.253 −2.047 209003_at SLC25A11 chr17p13.3 0.726 −0.089 −2.046 205399_at DCLK1 chr13q13 0.848 0.234 −2.046 205029_s_at FABP7 chr6q22-q23 0.906 0.460 −2.046 211016_x_at HSPA4 chr5q31.1-q31.2 0.715 −0.110 −2.044 211547_s_at PAFAH1B1 chr17p13.3 0.716 −0.106 −2.040 203727_at SKIV2L chr6p21 0.772 0.020 −2.040 206232_s_at B4GALT6 chr18q11 0.767 0.008 −2.037 214512_s_at SUB1 chr5p13.3 0.798 0.089 −2.036 217840_at DDX41 chr5q35.3 0.822 0.157 −2.036 202941_at NDUFV2 chr18p11.31-p11.2 0.862 0.289 −2.035 202671_s_at PDXK chr21q22.3 0.701 −0.134 −2.032 206436_at MPPED1 chr22q13.31 0.806 0.112 −2.030 203618_at FAIM2 chr12q13 0.614 −0.279 −2.029 217448_s_at LOC285412 /// chr14q11.2 /// 0.742 −0.045 −2.029 TOX4 chr4q25 210103_s_at FOXA2 chr20p11 0.720 −0.094 −2.029 216462_at — — 0.658 −0.209 −2.029 208536_s_at BCL2L11 chr2q13 0.561 −0.351 −2.028 208122_x_at KIR2DS3 chr19q13.4 0.583 −0.322 −2.027 208733_at RAB2A chr8q12.1 0.748 −0.032 −2.027 207971_s_at CEP68 chr2p14 0.614 −0.278 −2.027 218163_at MCTS1 chrXq22-q24 0.785 0.058 −2.026 211210_x_at SH2D1A chrXq25-q26 0.505 −0.417 −2.026 214444_s_at PVR chr19q13.2 0.546 −0.369 −2.026 211680_at PDLIM5 chr4q22 0.535 −0.382 −2.026 201248_s_at SREBF2 chr22q13 0.793 0.079 −2.025 201772_at AZIN1 chr8q22.3 0.729 −0.071 −2.023 221115_s_at LENEP chr1q22 0.649 −0.221 −2.022 209825_s_at UCK2 chr1q23 0.760 −0.001 −2.022 213404_s_at RHEB chr7q36 0.804 0.112 −2.020 211685_s_at NCALD chr8q22.2 0.604 −0.289 −2.020 211630_s_at GSS chr20q11.2 0.749 −0.026 −2.020 203843_at RPS6KA3 chrXp22.2-p22.1 0.878 0.356 −2.020 202178_at PRKCZ chr1p36.33-p36.2 0.745 −0.036 −2.019 216105_x_at PPP2R4 chr9q34 0.632 −0.246 −2.019 212431_at HMGXB3 chr5q33.1 0.677 −0.171 −2.019 208833_s_at ATXN10 chr22q13.31 0.833 0.199 −2.019 202780_at OXCT1 chr5p13.1 0.795 0.090 −2.018 202264_s_at TOMM40 chr19q13 0.747 −0.030 −2.017 206196_s_at RUNDC3A chr17q21.31 0.815 0.147 −2.016 211426_x_at GNAQ chr9q21 0.621 −0.262 −2.016 210689_at CLDN14 chr21q22.3 0.730 −0.066 −2.015 215406_at — — 0.603 −0.287 −2.014 202228_s_at NPTN chr15q22 0.825 0.175 −2.014 202499_s_at SLC2A3 chr12p13.3 0.792 0.084 −2.013 208898_at ATP6V1D chr14q23-q24.2 0.834 0.206 −2.013 214681_at GK chrXp21.3 0.691 −0.142 −2.013 214348_at TACR2 chr10q11-q21 0.528 −0.384 −2.010 203114_at SSSCA1 chr11q13.1 0.775 0.041 −2.010 204048_s_at PHACTR2 chr6q24.2 0.560 −0.344 −2.010 217077_s_at GABBR2 chr9q22.1-q22.3 0.756 −0.005 −2.010 213909_at LRRC15 chr3q29 0.619 −0.261 −2.009 216298_at TRGV5 chr7p14 0.655 −0.205 −2.009 211017_s_at NF2 chr22q12.2 0.711 −0.103 −2.009 209445_x_at C7orf44 chr7p13 0.741 −0.038 −2.008 213262_at SACS chr13q12 0.789 0.079 −2.008 206690_at ACCN1 chr17q12 0.867 0.318 −2.008 221504_s_at ATP6V1H chr8q11.2 0.823 0.173 −2.007 219054_at C5orf23 chr5p13.3 0.608 −0.277 −2.007 205820_s_at APOC3 chr11q23.1-q23.2 0.650 −0.212 −2.006 202143_s_at COPS8 chr2q37.3 0.662 −0.191 −2.006 204216_s_at ZC3H14 chr14q31.3 0.710 −0.102 −2.005 219767_s_at CRYZL1 chr21q21.3 0.811 0.139 −2.005 208462_s_at ABCC9 chr12p12.1 0.687 −0.145 −2.005 214260_at COPS8 chr2q37.3 0.815 0.151 −2.004 204521_at C12orf24 chr12q24.11 0.841 0.232 −2.003 210720_s_at NECAB3 chr20q11.22 0.731 −0.058 −2.003 213200_at SYP chrXp11.23-p11.22 0.811 0.140 −2.003 208778_s_at TCP1 chr6q25.3-q26 0.797 0.101 −2.002 219600_s_at TMEM50B chr21q22.11 0.738 −0.043 −2.002 210123_s_at

7A /// chr15q13.1 /// 0.755 −0.003 −2.002 CHRNA7 /// chr15q14 LO

209934_s_at ATP2C1 chr3q22.1 0.560 −0.341 −2.002 218918_at MAN1C1 chr1p35 0.826 0.185 −2.000 207026_s_at ATP2B3 chrXq28 0.668 −0.178 −2.000 214160_at — — 0.653 −0.204 −2.000 36994_at ATP6V0C chr16p13.3 0.773 0.040 −1.998 204049_s_at PHACTR2 chr6q24.2 0.634 −0.234 −1.998 220928_s_at PRDM16 chr1p36.23-p33 0.799 0.109 −1.997 203237_s_at NOTCH3 chr19p13.2-p13.1 0.560 −0.339 −1.997 203303_at DYNLT3 chrXp21 0.840 0.231 −1.997 208398_s_at TBPL1 chr6q22.1-q22.3 0.823 0.178 −1.996 206197_at NME5 chr5q31 0.765 0.022 −1.996 216786_at LOC159110 chrYq11.221 0.651 −0.205 −1.996 204812_at ZW10 chr11q23.2 0.827 0.192 −1.996 216643_at — — 0.652 −0.203 −1.995 218547_at DHDDS chr1p36.11 0.895 0.433 −1.994 215227_x_at ACP1 chr2p25 0.718 −0.080 −1.994 219033_at PARP8 chr5q11.1 0.739 −0.036 −1.994 217881_s_at CDC27 chr17q12-q23.2 0.768 0.031 −1.993 201431_s_at DPYSL3 chr5q32 0.842 0.239 −1.993 221127_s_at DKK3 chr11p15.2 0.821 0.175 −1.993 221251_x_at INO80B chr2p13.1 0.873 0.346 −1.992 214665_s_at CHP chr15q13.3 0.819 0.170 −1.992 221839_s_at UBAP2 chr9p13.3 0.830 0.204 −1.991 206452_x_at PPP2R4 chr9q34 0.648 −0.207 −1.990 206051_at ELAVL4 chr1p34 0.860 0.301 −1.990 216686_at FLJ40330 chr2p11.2 0.705 −0.104 −1.989 202166_s_at PPP1R2 chr3q29 0.755 0.003 −1.988 210460_s_at PSMD4 chr1q21.2 0.851 0.272 −1.988 210450_at LOC90925 chr14q32.33 0.649 −0.204 −1.987 211883_x_at CEACAM1 chr19q13.2 0.789 0.088 −1.987 205233_s_at PAFAH2 chr1p36 0.709 −0.095 −1.986 214074_s_at CTTN chr11q13 0.740 −0.029 −1.986 214728_x_at SMARCA4 chr19p13.2 0.769 0.037 −1.986 212862_at CDS2 chr20p13 0.809 0.143 −1.985 220570_at RETN chr19p13.2 0.695 −0.121 −1.984 204953_at SNAP91 chr6q14.2 0.827 0.195 −1.984 203810_at DNAJB4 chr1p31.1 0.637 −0.223 −1.984 211662_s_at VDAC2 chr10q22 0.804 0.129 −1.984 208093_s_at NDEL1 chr17p13.1 0.802 0.124 −1.984 215093_at NSDHL chrXq28 0.760 0.018 −1.984 204622_x_at NR4A2 chr2q22-q23 0.930 0.592 −1.983 89948_at PCIF1 chr20q13.12 0.689 −0.132 −1.983 204169_at IMPDH1 chr7q31.3-q32 0.875 0.359 −1.982 207928_s_at GLRA3 chr4q33-q34 0.685 −0.139 −1.982 219005_at TMEM59L chr19p12 0.755 0.007 −1.982 203894_at TUBG2 chr17q21 0.723 −0.063 −1.981 210098_s_at — — 0.683 −0.142 −1.981 212855_at DCUN1D4 chr4q12 0.819 0.174 −1.981 214231_s_at KIAA0564 chr13q14.11 0.504 −0.400 −1.980 208121_s_at PTPRO chr12p13.3- 0.853 0.280 −1.980 p13.2|12p13-p12 207853_s_at SNCB chr5q35 0.785 0.081 −1.980 218503_at KIAA1797 chr9p21 0.826 0.194 −1.980 214641_at COL4A3 chr2q36-q37 0.662 −0.178 −1.979 208864_s_at TXN chr9q31 0.806 0.138 −1.979 208699_x_at TKT chr3p14.3 0.632 −0.228 −1.979 212271_at MAPK1 chr22q11.2|22q11.21 0.775 0.055 −1.978 220069_at TUBA8 chr22q11.1 0.551 −0.342 −1.977 218609_s_at NUDT2 chr9p13 0.588 −0.292 −1.976 212600_s_at UQCRC2 chr16p12 0.772 0.050 −1.976 221721_s_at LZTS1 chr8p22 0.691 −0.125 −1.976 212764_at ZEB1 chr10p11.2 0.787 0.088 −1.975 216286_at — — 0.793 0.103 −1.975 50314_i_at C20orf27 chr20p13 0.849 0.270 −1.975 216323_x_at TUBA3D chr2q21.1 0.606 −0.265 −1.975 210676_x_at

PD5 /// chr2q13 0.682 −0.141 −1.974 RGPD6 /// RG

211729_x_at BLVRA chr7p14-cen 0.819 0.178 −1.973 218681_s_at SDF2L1 chr22q11.21 0.632 −0.225 −1.973 203001_s_at STMN2 chr8q21.13 0.846 0.261 −1.973 212518_at PIP5K1C chr19p13.3 0.851 0.280 −1.972 218421_at CERK chr22q13.31 0.879 0.380 −1.972 202791_s_at SAPS2 chr22q13.33 0.572 −0.312 −1.972 202460_s_at LPIN2 chr18p11.31 0.886 0.406 −1.972 216266_s_at ARFGEF1 chr8q13 0.684 −0.135 −1.971 204525_at PHF14 chr7p21.3 0.644 −0.205 −1.970 210416_s_at CHEK2 chr22q11|22q12.1 0.643 −0.205 −1.970 202967_at GSTA4 chr6p12.1 0.750 0.002 −1.969 212984_at ATF2 chr2q32 0.857 0.301 −1.969 202281_at GAK chr4p16 0.773 0.057 −1.965 203945_at ARG2 chr14q24.1-q24.3 0.696 −0.109 −1.965 202472_at MPI chr15q22-qter 0.723 −0.056 −1.965 205737_at KCNQ2 chr20q13.3 0.800 0.128 −1.965 217187_at MUC5AC chr11p15.5 0.538 −0.353 −1.964 210335_at RASSF9 chr12q21.31 0.644 −0.202 −1.963 213103_at STARD13 chr13q12-q13 −0.846 0.817 4.840 219728_at MYOT chr5q31 −0.695 0.725 3.598 208214_at ADRB1 chr10q24-q26 −0.658 0.733 3.493 208371_s_at RING1 chr6p21.3 −0.682 0.711 3.490 213185_at KIAA0556 chr16p12.1-p11.2 −0.811 0.530 3.485 203648_at TATDN2 chr3p25.3 −0.631 0.706 3.290 209289_at NFIB chr9p24.1 −0.734 0.584 3.255 220739_s_at CNNM3 chr2p12-p11.2 −0.752 0.547 3.225 205909_at POLE2 chr14q21-q22 −0.775 0.506 3.222 200601_at ACTN4 chr19q13 −0.717 0.592 3.207 218245_at TSKU chr11q13.5 −0.716 0.591 3.199 211494_s_at SLC4A4 chr4q21 −0.718 0.582 3.178 218723_s_at C13orf15 chr13q14.11 −0.654 0.639 3.116 203298_s_at JARID2 chr6p24-p23 −0.527 0.733 3.081 209290_s_at NFIB chr9p24.1 −0.734 0.511 3.044 209049_s_at ZMYND8 chr20q13.12 −0.672 0.585 3.009 207663_x_at GAGE3 chrXp11.4-p11.2 −0.705 0.537 2.993 208755_x_at

A /// chr17q25 /// −0.537 0.699 2.970 H3F3B /// chr1q41 /// LOC44

chr2q31.1 91617_at DGCR8 chr22q11.2 −0.603 0.636 2.936 219584_at PLA1A chr3q13.13-q13.2 −0.443 0.747 2.923 208190_s_at LSR chr19q13.12 −0.644 0.590 2.922 219000_s_at DSCC1 chr8q24.12 −0.689 0.529 2.907 213972_at FOXD1 chr5q12-q13 −0.647 0.570 2.873 204075_s_at KIAA0562 chr1p36.32 −0.663 0.541 2.845 212144_at UNC84B chr22q13.1 −0.635 0.564 2.813 204457_s_at GAS1 chr9q21.3-q22 −0.256 0.810 2.810 212684_at ZNF3 chr7q22.1 −0.669 0.511 2.784 218880_at FOSL2 chr2p23.3 −0.441 0.715 2.776 209684_at RIN2 chr20p11.22 −0.545 0.640 2.773 39318_at TCL1A chr14q32.1 −0.497 0.676 2.770 201502_s_at NFKBIA chr14q13 −0.447 0.709 2.767 213541_s_at ERG chr21q22.3 −0.591 0.595 2.766 204535_s_at REST chr4q12 −0.613 0.571 2.759 200621_at CSRP1 chr1q32 −0.625 0.556 2.755 207793_s_at EPB41 chr1p33-p32 −0.532 0.637 2.728 216452_at TRPM3 chr9q21.11-q21.12 −0.523 0.643 2.723 201876_at PON2 chr7q21.3 −0.632 0.534 2.717 206026_s_at TNFAIP6 chr2q23.3 −0.286 0.773 2.679 209544_at RIPK2 chr8q21 −0.528 0.625 2.677 207761_s_at METTL7A chr12q13.13 −0.474 0.667 2.676 207961_x_at MYH11 chr16p13.11 −0.502 0.644 2.668 205112_at PLCE1 chr10q23 −0.550 0.602 2.663 209710_at GATA2 chr3q21.3 −0.514 0.629 2.651 204187_at GMPR chr6p23 −0.604 0.543 2.651 203297_s_at JARID2 chr6p24-p23 −0.537 0.609 2.648 201497_x_at MYH11 chr16p13.11 −0.596 0.551 2.647 214393_at RND2 chr17q21 −0.588 0.557 2.639 204373_s_at CEP350 chr1p36.13-q41 −0.579 0.564 2.632 209032_s_at CADM1 chr11q23.2 −0.563 0.577 2.623 218656_s_at LHFP chr13q12 −0.270 0.765 2.602 216320_x_at MST1 chr3p21 −0.575 0.550 2.581 208718_at DDX17 chr22q13.1 −0.497 0.619 2.570 215038_s_at SETD2 chr3p21.31 −0.329 0.726 2.556 200915_x_at KTN1 chr14q22.1 −0.560 0.554 2.548 201845_s_at RYBP chr3p13 −0.338 0.718 2.542 213638_at PHACTR1 chr6p24.1 −0.562 0.551 2.541 49452_at ACACB chr12q24.11 −0.533 0.578 2.538 202173_s_at VEZF1 chr17q22 −0.401 0.679 2.536 201361_at TMEM109 chr11q12.2 −0.517 0.588 2.526 214703_s_at MAN2B2 chr4p16.1 −0.569 0.533 2.513 213891_s_at TCF4 chr18q21.1 −0.585 0.514 2.511 203685_at BCL2 chr18q21.33|18q21.3 −0.499 0.598 2.509 213828_x_at

A /// chr17q25 /// −0.470 0.619 2.500 H3F3B /// chr1q41 /// LOC44

chr2q31.1 207191_s_at ISLR chr15q23-q24 −0.310 0.721 2.493 212237_at ASXL1 chr20q11.1 −0.074 0.817 2.478 210451_at PKLR chr1q21 −0.397 0.663 2.467 201739_at SGK1 chr6q23 −0.482 0.596 2.459 207390_s_at SMTN chr22q12.2 −0.531 0.550 2.450 207016_s_at ALDH1A2 chr15q22.1 −0.558 0.517 2.435 200665_s_at SPARC chr5q31.3-q32 −0.561 0.513 2.433 204225_at HDAC4 chr2q37.3 −0.185 0.765 2.419 217118_s_at C22orf9 chr22q13.31 −0.495 0.570 2.410 202294_at STAG1 chr3q22.3 −0.067 0.808 2.409 217856_at RBM8A chr1q12 −0.517 0.548 2.408 32069_at N4BP1 chr16q12.1 −0.504 0.559 2.403 219851_at ZNF613 chr19q13.33 −0.541 0.521 2.399 217367_s_at ZHX3 chr20q12 −0.382 0.653 2.396 207404_s_at HTR1E chr6q14-q15 −0.426 0.621 2.392 221087_s_at APOL3 chr22q13.1 −0.464 0.590 2.392 211940_x_at

A /// chr17q25 /// −0.326 0.681 2.370 H3F3B /// chr1q41 /// LOC44

chr2q31.1 216264_s_at LAMB2 chr3p21 −0.287 0.703 2.369 202332_at CSNK1E chr22q13.1 −0.484 0.564 2.366 215146_s_at TTC28 chr22q12.1 −0.422 0.615 2.363 205053_at PRIM1 chr12q13 −0.345 0.665 2.353 200610_s_at NCL chr2q12-qter −0.075 0.795 2.349 219255_x_at IL17RB chr3p21.1 −0.212 0.735 2.340 219371_s_at KLF2 chr19p13.13-p13.11 −0.517 0.522 2.334 203010_at STAT5A chr17q11.2 −0.480 0.556 2.328 219213_at JAM2 chr21q21.2 −0.373 0.633 2.308 218089_at C20orf4 chr20pter-q12 −0.248 0.707 2.298 210147_at ART3

hr4p15.1- −0.510 0.516 2.298 p14|4p15.1- p14|4p15.1-p1

208763_s_at TSC22D3 chrXq22.3 −0.358 0.640 2.295 213467_at RND2 chr17q21 −0.330 0.655 2.284 212655_at ZCCHC14 chr16q24.2 −0.249 0.703 2.284 213765_at MFAP5 chr12p13.1-p12.3 −0.419 0.588 2.270 205907_s_at OMD chr9q22.31 −0.482 0.532 2.267 202172_at VEZF1 chr17q22 −0.403 0.596 2.257 203045_at NINJ1 chr9q22 −0.405 0.586 2.231 203694_s_at DHX16 chr6p21.3 0.093 0.831 2.228 218963_s_at KRT23 chr17q21.2 −0.305 0.654 2.224 212747_at ANKS1A chr6p21.31 −0.208 0.708 2.218 209030_s_at CADM1 chr11q23.2 −0.308 0.649 2.215 213401_s_at TBL1X chrXp22.3 −0.394 0.589 2.214 209546_s_at APOL1 chr22q13.1 −0.465 0.528 2.210 209497_s_at RBM4B chr11q13 −0.128 0.744 2.204 202925_s_at PLAGL2 chr20q11.21 −0.481 0.511 2.204 204731_at TGFBR3 chr1p33-p32 −0.435 0.552 2.203 209815_at PTCH1 chr9q22.3 −0.239 0.687 2.202 214721_x_at CDC42EP4 chr17q24-q25 −0.333 0.630 2.202 218062_x_at CDC42EP4 chr17q24-q25 −0.331 0.630 2.201 203449_s_at TERF1 chr8q13 −0.458 0.530 2.200 212618_at ZNF609 chr15q22.31 −0.392 0.586 2.199 203038_at PTPRK chr6q22.2-q22.3 −0.426 0.557 2.197 218829_s_at CHD7 chr8q12.2 −0.379 0.589 2.179 221924_at ZMIZ2 chr7p13 −0.340 0.617 2.178 204872_at TLE4 chr9q21.31 −0.368 0.595 2.170 212977_at CXCR7 chr2q37.3 −0.337 0.613 2.157 217853_at TNS3 chr7p12.3 −0.214 0.688 2.152 220032_at C7orf58 chr7q31.31 −0.461 0.509 2.148 219860_at LY6G5C chr6p21.33 −0.162 0.714 2.146 57532_at DVL2 chr17p13.2 −0.150 0.719 2.142 212387_at TCF4 chr18q21.1 −0.463 0.502 2.134 219948_x_at UGT2A3 chr4q13.2 −0.443 0.520 2.131 205932_s_at MSX1 chr4p16.3-p16.1 −0.448 0.512 2.123 218839_at HEY1 chr8q21 −0.270 0.646 2.120 201938_at CDK2AP1 chr12q24.31 0.137 0.829 2.119 208999_at 8-Sep chr5q31 0.021 0.787 2.113 206038_s_at NR2C2 chr3p25 −0.415 0.537 2.110 212816_s_at CBS chr21q22.3 −0.383 0.557 2.091 206134_at ADAMDEC1 chr8p21.2 −0.396 0.546 2.091 218400_at OAS3 chr12q24.2 −0.312 0.608 2.083 213380_x_at MSTP9 chr1p36.13 −0.408 0.531 2.078 208919_s_at NADK chr1p36.33-p36.21 −0.015 0.765 2.076 204327_s_at ZNF202 chr11q23.3 −0.057 0.747 2.073 206504_at CYP24A1 chr20q13 −0.436 0.502 2.066 46665_at SEMA4C chr2q11.2 −0.303 0.608 2.063 218413_s_at ZNF639 chr3q26.32 −0.262 0.634 2.057 217905_at C10orf119 chr10q26.11 −0.295 0.611 2.056 201983_s_at EGFR chr7p12 −0.277 0.623 2.055 212238_at ASXL1 chr20q11.1 −0.131 0.707 2.053 217184_s_at LTK chr15q15.1-q21.1 −0.280 0.620 2.052 208818_s_at COMT chr22q11.21- −0.326 0.588 2.052 q11.23|22q11.21 44783_s_at HEY1 chr8q21 −0.313 0.594 2.043 212848_s_at C9orf3 chr9q22.32 −0.392 0.532 2.041 202866_at DNAJB12 chr10q22.1 −0.236 0.644 2.038 203959_s_at ZBTB40 chr1pter-q31.3 −0.231 0.646 2.035 206919_at ELK4 chr1q32 −0.387 0.533 2.031 202411_at IFI27 chr14q32 −0.349 0.563 2.030 212447_at KBTBD2 chr7p14.3 −0.269 0.621 2.030 204638_at ACP5 chr19p13.3-p13.2 −0.371 0.545 2.029 214857_at — — −0.309 0.590 2.021 213058_at TTC28 chr22q12.1 −0.194 0.664 2.021 212321_at SGPL1 chr10q21 −0.226 0.645 2.019 221012_s_at TRIM8 chr10q24.3 −0.140 0.692 2.014 212385_at TCF4 chr18q21.1 −0.392 0.522 2.013 203117_s_at PAN2 chr12q13.2-q13.3 −0.373 0.537 2.010 200659_s_at PHB chr17q21 −0.098 0.713 2.008 221824_s_at 8-Mar chr10q11.21 0.085 0.791 2.002 221252_s_at GSG1 chr12p13.1 −0.399 0.508 1.989 201783_s_at RELA chr11q13 −0.390 0.515 1.989 206747_at GPRIN2 chr10q11.22 −0.392 0.511 1.981 206402_s_at NPFF chr12q13.13 −0.121 0.692 1.972 54051_at PKNOX1 chr21q22.3 −0.083 0.711 1.972 203617_x_at ELK1 chrXp11.2 −0.319 0.566 1.968 209343_at EFHD1 chr2q37.1 −0.374 0.520 1.965 209427_at SMTN chr22q12.2 −0.343 0.545 1.964

indicates data missing or illegible when filed

SUPPLEMENTARY TABLE 8 This file contains the lists of genes differentially correlated with aSynL in rs356168 CCvsTT non PD-affected cortex samples. 8 Illumina Correlation wit aSynL Probe Gene Symbol Cytoband rs356168 CC rs356168 TT Diff. Score GI_14589898-S MAP2K1 15q22.1-q22.3

0.898 0.961 −2.399 GI_4557816-S OXCT 5p13.1 0.863 0.944 −2.267 GI_4507878-S VDAC1 5q31 0.669 0.944 −4.643 GI_16579891-A WDR7 18q21.1-q22 0.861 0.944 −2.282 GI_37549342-S KIAA1265 2q32.3 0.838 0.937 −2.395 GI_18765734-A SNAP25 20p12-p11.2 0.852 0.936 −2.135 GI_41406092-I JDP1 10q22.1 0.852 0.935 −2.104 GI_21361889-S KLHL12 1q32.1 0.811 0.935 −2.727 GI_21536456-S MOAP1 14q32 0.776 0.935 −3.191 GI_19913423-S ATP6V1A 3q13.2-q13.31 0.820 0.934 −2.576 GI_21735619-S MDH1 2p13.3 0.802 0.930 −2.651 GI_42558244-S GMRP-1 11p15.2 0.758 0.928 −3.135 GI_12597656-S FLJ13110 2p11.2 0.782 0.928 −2.845 GI_34147658-S UCHL1 4p14 0.840 0.926 −1.961 GI_20357538-A ATP6V1G2 6p21.3 0.794 0.926 −2.616 GI_31542527-S DKFZP566B183 12p13.31 0.833 0.925 −2.054 GI_6042206-S RAM 12q24.3 0.811 0.924 −2.347 GI_7770073-A IARS 9q21 0.745 0.924 −3.140 GI_19745179-S MO25 2q37.1 0.794 0.922 −2.500 GI_21614509-A FGF12 3q28 0.726 0.921 −3.245 GI_29744077-S LOC340542 Xq22.1 0.826 0.920 −1.992 GI_31341302-S JAZF1 7p15.2-p15.1 0.715 0.920 −3.321 GI_21464140-I AKAP11 13q14.11 0.785 0.919 −2.528 GI_24308335-S C6orf168 6q16.2-q16.3 0.813 0.917 −2.094 GI_19718771-A ASNS 7q21.3 0.801 0.916 −2.227 GI_4758177-S DNG1 7q21.3-q22.1 0.803 0.916 −2.194 GI_41352714-S VPS35 16q12 0.787 0.915 −2.363 GI_31341108-S LOC170261 Xq24 0.720 0.914 −3.111 GI_15451903-S MOX2 3q12-q13 0.790 0.914 −2.324 GI_42544237-S DCAMKL1 13q13 0.724 0.910 −2.945 GI_37543748-S KIAA1467 12p13.1 0.716 0.910 −3.019 GI_15011917-S ATP6AP2 Xp11.4 0.618 0.908 −3.817 GI_16950592-I MRPS21 null 0.759 0.907 −2.481 GI_21361148-S RGS7 1q43 0.763 0.906 −2.411 GI_38257145-S LOC157567 8q22.3 0.787 0.904 −2.060 GI_27734858-S LOC285533 4q31.3 0.783 0.900 −2.019 GI_38201693-S RGS4 1q23.3 0.780 0.898 −1.994 GI_4502806-S CHGB 20pter-p12 0.732 0.896 −2.497 GI_27501445-S DENR 12q24.31 0.767 0.895 −2.091 GI_33946322-S ARL1 12q23.2 0.701 0.895 −2.768 GI_7106298-S E46L 22q13.31 0.721 0.895 −2.573 GI_21536422-A AM PH 7p14-p13 0.739 0.894 −2.382 GI_23110933-A PSMA1 11p15.1 0.630 0.894 −3.367 GI_37546739-S KIAA1107 1p22.1 0.699 0.893 −2.738 GI_7657043-S NGFRAP1 Xq22.2 0.696 0.892 −2.754 GI_22094078-S TRIP3 17q12 0.707 0.892 −2.652 GI_34222111-S DKFZp547C176 11q22.3 0.767 0.892 −2.008 GI_19482173-S CUL2 10p11.21 0.654 0.890 −3.089 GI_29740938-S KIAA1136 10p12.1 0.690 0.890 −2.760 GI_27886536-1 ATP2A2 12q23-q24.1 0.730 0.889 −2.348 GI_24462252-S ZNF25 10p11.21 0.737 0.888 −2.256 GI_4755130-S CCK 3p22-p21.3 0.745 0.885 −2.101 GI_24475639-S HSA272196 17q11.2 0.718 0.885 −2.377 GI_41350195-S RAB1A 2p14 0.716 0.884 −2.383 GI_13899218-S GABARAPL1 12p13.2 0.722 0.884 −2.324 GI_41281397-S SHOC2 10q25 0.737 0.883 −2.146 GI_15147227-S BEX1 Xq21-q23 0.505 0.883 −4.014 GI_24475709-S HBLD2 9q21.33 0.748 0.880 −1.971 GI_17999531-S COX6C 8q22-q23 0.572 0.880 −3.495 GI_5730086-S TCTE1L Xp21 0.626 0.880 −3.088 GI_4504066-S GOT1 10q24.1-q25.1 0.647 0.879 −2.893 GI_5730054-S PLK2 5q12.1-q13.2 0.731 0.879 −2.116 GI_10800415-S SCG2 2q35-q36 0.538 0.878 −3.692 GI_21362111-S C7orf2 7q36 0.708 0.878 −2.330 GI_39930462-S KIAA1701 Xq23 0.557 0.878 −3.550 GI_24415993-S SFRS7 2p22.1 0.597 0.877 −3.242 GI_14769619-S KIAA1701 Xq23 0.724 0.877 −2.142 GI_1321582-S SUCLA2 13q12.2-q13.3 0.643 0.873 −2.798 GI_8922171-S DKFZp761K1423 8p22 0.692 0.873 −2.369 GI_33147079-S AMSH-LP 10q23.31 0.623 0.873 −2.956 GI_18426903-A WRNIP1 6p25.2 0.712 0.872 −2.167 GI_5031710-S GC20 3p22.1 0.717 0.872 −2.112 GI_19923783-S PC4 5p13.3 0.729 0.872 −1.981 GI_21464100-S YWHAG 7q11.23 0.573 0.869 −3.257 GI_20531764-S C13orf1 13q14 0.721 0.868 −2.006 GI_22907051-S ARPC1A 7q22.1 0.717 0.867 −2.023 GI_29135342-S HINT1 5q31.2 0.638 0.866 −2.711 GI_16554603-S MRPS23 17q22-q23 0.692 0.866 −2.236 GI_32698731-S KIAA1363 3q26.31 0.660 0.866 −2.512 GI_6466447-S DSTN 20p12.1 0.647 0.865 −2.613 GI_44771179-S NACSIN 2p15 0.711 0.865 −2.032 GI_4758733-S PMPCB 7q22.1 0.685 0.865 −2.278 GI_28461128-S ANKMY2 7p21 0.582 0.864 −3.095 GI_21265077-S MRPL15 8q11.2-q13 0.632 0.864 −2.705 GI_12232400-S SMYD3 1q44 0.459 0.863 −3.892 GI_4502300-S ATP5G3 2q31.1 0.693 0.862 −2.157 GI_6005992-I CLTA 9p13 0.559 0.862 −3.216 GI_4885078-S ATP5C1 10p15.1 0.646 0.861 −2.537 GI_19923737-S PRPS1 Xq21.32-q24 0.553 0.860 −3.232 GI_38327553-S GABRA1 5q34-q35 0.484 0.860 −3.674 GI_30089947-S PPM1E 17q22 0.586 0.858 −2.958 GI_30425545-S C14orf11 14q13.1 0.637 0.857 −2.538 GI_4505812-S DNCL1 12q24.23 0.571 0.856 −3.028 GI_34222347-S LRP11 6q25.1 0.670 0.855 −2.220 GI_5453602-S CCT2 12q15 0.617 0.854 −2.651 GI_31652246-S STXBP5 6q24.3 0.572 0.853 −2.964 GI_28872807-S GAP43 3q13.1-q13.2 0.661 0.849 −2.206 GI_20357567-S AASDHPPT 11q22 0.631 0.849 −2.447 GI_41150497-S LOC283951 16p13.3 0.503 0.847 −3.335 GI_8922423-S GSPT2 Xp11.23-p11.2

0.667 0.847 −2.115 GI_33359693-A UBE2E3 2q32.1 0.675 0.846 −2.034 GI_6806896-I SNCA 4q21 0.668 0.846 −2.089 GI_21626459-S AF1Q 1q21 0.539 0.846 −3.068 GI_13376622-S NIF3L1BP1 3p14.1 0.641 0.845 −2.300 GI_38373689-S COPS4 4q21.22 0.662 0.845 −2.124 GI_41281529-S FAM20B 1q25 0.637 0.845 −2.327 GI_24371267-S NAP1L5 4q22.1 0.669 0.843 −2.025 GI_7108354-S LMO4 1p22.3 0.648 0.843 −2.200 GI_4507310-S SUPT4H1 17q21-q23 0.627 0.842 −2.361 GI_24308441-S C6orf117 6q14.3 0.620 0.841 −2.403 GI_37059725-S GRPEL1 4p16 0.446 0.840 −3.560 GI_41349455-S PREP 6q22 0.581 0.839 −2.658 GI_29789280-S KIAA1750 8q22.1 0.620 0.839 −2.364 GI_23065568-S GSTA4 6p12.1 0.625 0.838 −2.318 GI_24475618-S CD83 6p23 0.643 0.838 −2.172 GI_24308232-S SYT13 11p12-p11 0.569 0.837 −2.717 GI_6912611-A PSK-1 16p11.2 0.647 0.836 −2.110 GI_7706752-S UCHL5 1q32 0.664 0.836 −1.965 GI_21327696-S DDX25 11q24 0.654 0.836 −2.050 GI_40317631-S NUDT4 12q21 0.621 0.836 −2.309 GI_13375741-S FLJ11712 13q14.3 0.657 0.835 −1.997 GI_14249303-S MGC12966 7p22.1 0.607 0.835 −2.401 GI_17017986-S COX5A 15q25 0.526 0.833 −2.959 GI_4506064-S PRKAR2B 7q22 0.641 0.833 −2.115 GI_38569420-S ACLY 17q12-q21 0.641 0.833 −2.108 GI_19923976-S C7orf30 7p15.3 0.604 0.833 −2.393 GI_4507728-S TUBB 6p25 0.558 0.833 −2.727 GI_4503064-S CRYM 16p13.11-p12.

0.531 0.832 −2.907 GI_25014108-S SELH 11q12.1 0.508 0.832 −3.058 GI_34452698-S ACTR3 2q14.1 0.638 0.832 −2.114 GI_31377757-S AFTIPHILIN 2p14 0.611 0.832 −2.323 GI_4506930-S SH3GL2 9p22 0.598 0.827 −2.347 GI_19923361-S THY1 11q22.3-q23 0.622 0.825 −2.139 GI_31542788-S ABHD7 1p22.1 0.478 0.825 −3.138 GI_21264557-S SMAP1 6q13 0.397 0.825 −3.614 GI_16950602-S MRPS35 12p11 0.599 0.824 −2.303 GI_7657624-S STAU2 8q13-q21.1 0.622 0.824 −2.125 GI_22027631-I DGKB 7p21.2 0.623 0.824 −2.113 GI_21361451-S GLS 2q32-q34 0.622 0.824 −2.116 GI_20336745-A H2AFY 5q31.3-q32 0.464 0.821 −3.161 GI_34335244-A NMNAT2 1q25 0.550 0.821 −2.604 GI_38788154-1 GABRG2 5q31.1-q33.1 0.529 0.819 −2.725 GI_41393590-S API5 11p11.2 0.599 0.819 −2.218 GI_13375984-S FLJ14007 8q21.13 0.539 0.819 −2.643 GI_38202242-S YARS 1p35.1 0.554 0.814 −2.482 GI_4505698-S PDHX 11p13 0.569 0.813 −2.358 GI_45359844-S G3BP2 4q21.1 0.402 0.813 −3.415 GI_21536251-S NBEA 13q13 0.530 0.811 −2.603 GI_20127465-S HOMER1 5q14.2 0.534 0.811 −2.574 GI_4557642-S HMGCR 5q13.3-q14 0.530 0.811 −2.594 GI_31341922-S LOC151963 3q29 0.462 0.810 −3.024 GI_4503352-S DOC2A 16p11.2 0.600 0.810 −2.092 GI_38261964-I ARPP-21 3p22.3 0.310 0.810 −3.880 GI_29244580-S HIP14 12q21.2 0.554 0.810 −2.416 GI_4506566-S RNMT 18p11.22-p11.

0.551 0.808 −2.414 GI_10938020-S FABP3 1p33-p32 0.483 0.806 −2.835 GI_42734437-S BM-009 8q24.21 0.568 0.806 −2.262 GI_32130513-A NDRG3 20q11.21-q11.

0.331 0.806 −3.709 GI_10092672-S LOC57019 16q13-q21 0.523 0.805 −2.563 GI_40316942-S ALAS1 3p21.1 0.482 0.804 −2.809 GI_4506456-S RCN2 15q23 0.598 0.804 −2.014 GI_23346425-S ATP5A1 18q12-q21 0.571 0.803 −2.199 GI_32189393-S ATP5B 12q13.13 0.346 0.799 −3.533 GI_11612654-S FXYD6 11q23.3 0.582 0.799 −2.070 GI_24475975-S TBC1D7 6p24.1 0.519 0.797 −2.481 GI_30260186-A ATPIF1 null 0.538 0.796 −2.334 GI_18105038-S COX7B Xq21.1 0.590 0.795 −1.960 GI_8922600-S ARL10C 3p26.2 0.443 0.793 −2.908 GI_30025025-S OSTM1 6q21 0.506 0.793 −2.505 GI_40805828-A COPS8 2q37.3 0.433 0.793 −2.956 GI_40316934-S ALS2 2q33.1 0.452 0.791 −2.824 GI_22095341-S CCT6A 7p11.2 0.302 0.791 −3.663 GI_25188178-S VDAC3 8p11.2 0.574 0.790 −2.010 GI_13994272-S C1QTNF4 11q11 0.472 0.790 −2.685 GI_23110938-A PSMA3 14q23 0.498 0.789 −2.516 GI_5031856-S LDHA 11p15.4 0.460 0.789 −2.741 GI_34304321-S MRPL45 17q21.2 0.356 0.788 −3.339 GI_5803110-S EBNA1BP2 1p35-p33 0.452 0.788 −2.782 GI_15147332-S TRIM37 17q23.2 0.576 0.788 −1.968 GI_5453857-S PCP4 21q22.2 0.234 0.787 −3.968 GI_19923458-S PAIP2 5q31.2 0.572 0.787 −1.988 GI_14251213-S DDX24 14q32 0.567 0.787 −2.018 GI_34222125-S RWDD2 6q14.2 0.516 0.786 −2.357 GI_16950656-S CCND2 12p13 0.367 0.786 −3.254 GI_25914753-A MKKS 20p12 0.459 0.785 −2.709 GI_4502202-S ARF3 12q13 0.419 0.784 −2.926 GI_42403584-A FHL2 2q12-q14 0.532 0.783 −2.215 GI_24041025-S NETO2 16q11 0.330 0.782 −3.408 GI_16933563-I DNM1L 12p11.21 0.556 0.780 −2.011 GI_34850060-S STMN2 8q21.13 0.549 0.779 −2.048 GI_29744085-S LOC340543 Xq22.1 0.412 0.778 −2.896 GI_5032234-S DSCR1L1 6p12.3 0.352 0.778 −3.232 GI_40255241-S SOD1 21q22.1 0.558 0.777 −1.963 GI_27436874-S RUNDC1 17q21.31 0.549 0.776 −2.019 GI_14149614-S MGC4189 17p13.2 0.433 0.776 −2.749 GI_10800414-S NDN 15q11.2-q12 0.548 0.776 −2.016 GI_14150131-S MGC12992 9q31.1 0.483 0.775 −2.434 GI_24496788-S LARS 5q32 0.378 0.775 −3.054 GI_23510242-S KIAA1797 9p21 0.487 0.772 −2.371 GI_37549357-S LOC375303 2q34 0.441 0.772 −2.649 GI_21314691-S HRMT1L3 12p13.3 0.520 0.771 −2.145 GI_34147353-S C7orf24 7p15-p14 0.517 0.769 −2.143 GI_42544158-S HSPH1 13q12.3 0.483 0.768 −2.342 GI_19923448-S DREV1 16p13-p12 0.351 0.766 −3.097 GI_32171224-S COQ3 6q16.3 0.519 0.766 −2.099 GI_19923444-A SPG3A 14q22.1 0.419 0.766 −2.713 GI_40217821-S SLITRK4 Xq2.7.3 0.517 0.765 −2.102 GI_21070966-A NRXN1 2p163 0.520 0.765 −2.070 GI_21361102-S SLC25A12 2q24 0.416 0.764 −2.709 GI_19913444-S HPCAL4 1p34.2 0.490 0.764 −2.261 GI_27734993-A SLC22A17 14q11.2 0.387 0.764 −2.867 GI_42558257-S FBXO33 14q21.1 0.417 0.763 −2.685 GI_21071040-S CNTNAP2 7q35-q36 0.505 0.762 −2.133 GI_34916055-I KNS2 14q32.3 0.523 0.761 −2.009 GI_40255108-S GRPEL2 5q33.1 0.433 0.761 −2.567 GI_15100150-S BAT5 6p21.3 0.433 0.760 −2.557 GI_6005726-S CCT8 21q22.11 0.516 0.759 −2.033 GI_34222355-S SIAH2 3q25 0.440 0.759 −2.504 GI_13325063-S CELSR2 1p21 0.202 0.758 −3.782 GI_11056011-S FLJ14084 Xq22.1 0.255 0.756 −3.493 GI_33519464-S NDUFA8 9q33.2-q34.11 0.462 0.754 −2.319 GI_38569472-S NDUFB1 14q32.12 0.490 0.754 −2.144 GI_21314723-S FLJ22490 8q13.2 0.351 0.753 −2.951 GI_7657479-S GHITM 10q23.1 0.464 0.753 −2.297 GI_33667026-S DC50 14q24.3 0.428 0.752 −2.502 GI_34878876-S NRN1 6p25.1 0.426 0.751 −2.500 GI_16950627-I AP1S1 7q22.1 0.491 0.750 −2.096 GI_40255259-S FLJ20701 2q36.3 0.478 0.748 −2.156 GI_31542934-S HLF 17q22 0.390 0.747 −2.665 GI_6382080-S RASGRP1 15q15 0.132 0.746 −3.999 GI_7705852-S DNCLI1 3p22.3 0.295 0.746 −3.172 GI_5453687-S HSPB3 5q11.2 0.390 0.746 −2.649 GI_14149608-S EXTL2 1p21 0.435 0.744 −2.368 GI_7662227-S SNAP91 6q14.2 0.390 0.743 −2.616 GI_31543422-S POLE3 9q33 0.388 0.742 −2.624 GI_21389510-S FLJ31121 5q31.3 0.448 0.740 −2.254 GI_21464102-S YWHAH 22q12.3 0.361 0.739 −2.735 GI_6005955-S DUSP12 1q21-q22 0.482 0.738 −2.025 GI_15451900-S KCNK1 1q42-q43 0.470 0.738 −2.092 GI_45007001-S LOC253782 2q24.3 0.422 0.738 −2.381 GI_21914880-S LGMN 14q32.1 0.356 0.737 −2.751 GI_21389358-S FLJ30525 1p13.3 0.484 0.737 −1.997 GI_31542152-S NPY 7p15.1 0.343 0.736 −2.814 GI_30795230-S BASP1 5p15.1-p14 0.379 0.735 −2.597 GI_19923309-S MCF2 Xq27 0.397 0.733 −2.483 GI_22749448-S C6orf65 6p12.1 0.469 0.733 −2.053 GI_13654273-S DKFZP566J2046 16p13.3 0.289 0.733 −3.067 GI_40254432-S SST 3q28 0.300 0.732 −2.994 GI_29568100-S ATP5L 11q23.3 0.478 0.731 −1.971 GI_4505684-S PDHA1 Xp22.2-p22.1 0.316 0.725 −2.843 GI_21536273-S CASQ1 1q21 0.408 0.725 −2.330 GI_4503874-S GAD2 10p11.23 0.078 0.724 −4.033 GI_44917605-S NAPB 20p12.3-p11.2

0.465 0.724 −1.985 GI_13384599-S SPATA7 14q31.3 0.311 0.723 −2.850 GI_32528285-A BACH 1p36.31-p36.1

0.351 0.723 −2.633 GI_19924138-S RAD23B 9q31.2 0.462 0.723 −1.987 GI_8923943-S NRF Xq24 0.265 0.721 −3.070 GI_18598508-S CDR2 16p12.3 0.368 0.720 −2.509 GI_20149591-S UNRIP 12p12.3 0.332 0.718 −2.686 GI_34222096-S KIAA0089 3p22.3 0.326 0.718 −2.715 GI_37551274-S LOC375489 6p25.2 0.104 0.717 −3.831 GI_5902001-S DUSP14 17q12 0.316 0.716 −2.755 GI_5174744-S UQCRH 1p33 0.347 0.716 −2.581 GI_37545060-S KIAA0802 18p11.22 0.424 0.714 −2.129 GI_5902095-S SMT3H1 21q22.3 0.425 0.711 −2.100 GI_40217822-S SLITRK5 13q31.2 0.373 0.711 −2.397 GI_8923764-S CACNA2D3 3p21.1 0.385 0.711 −2.323 GI_21361534-S HSPC138 11q14.2 0.435 0.709 −2.017 GI_24430185-S PIGC 1q23-q25 0.335 0.709 −2.583 GI_40353771-S BLVRA 7p14-cen 0.382 0.709 −2.322 GI_24308076-S C18orf10 18q12.2 0.416 0.709 −2.123 GI_40806213-S VIAAT 20q11.23 0.348 0.708 −2.499 GI_7706340-S CGI-127 2p23.1 0.154 0.707 −3.488 GI_22027654-S AP1S2 Xp22.2 0.016 0.705 −4.140 GI_14042922-S C9orf5 9q31 0.354 0.705 −2.435 GI_29728071-S KIAA0882 4q31.21 0.172 0.703 −3.359 GI_38201713-S ELAVL1 19p13.2 0.409 0.702 −2.105 GI_27436906-S MRPL49 11q13 0.321 0.702 −2.589 GI_20149593-S HSPCB 6p12 0.425 0.700 −1.990 GI_13375659-S FLJ22555 2q33.1 0.351 0.699 −2.403 GI_40254964-S FLJ11753 2q22.2-q22.3 0.419 0.699 −2.010 GI_37546515-S THOC2 Xq25-q26.3 0.425 0.698 −1.970 GI_14719429-S PNMA1 14q24.3 0.337 0.698 −2.464 GI_31542700-S AHI1 6q23.3 0.185 0.697 −3.249 GI_7661547-S CL25022 2q23.2 0.423 0.696 −1.965 GI_20336268-A GNB5 15q21.2 0.415 0.695 −1.995 GI_19923886-S DKFZp761H2121 10q26.13 0.013 0.694 −4.052 GI_36951161-S D4S234E 4p16.3 0.299 0.693 −2.621 GI_17017971-S RPL26L1 5q35.2 0.322 0.693 −2.498 GI_30794499-S AOF2 1p36.12 0.390 0.692 −2.116 GI_33667050-S DP1 5q22-q23 0.098 0.690 −3.609 GI_34147446-S MGC14288 12q13.13 0.331 0.690 −2.424 GI_7656945-S SLC30A9 4p13-p12 0.183 0.689 −3.177 GI_20127458-S CITED1 Xq13.1 0.253 0.689 −2.822 GI_31795541-A RFC5 12q24.2-q24.3 0.282 0.688 −2.667 GI_30158015-S KIAA1580 11p12 0.319 0.688 −2.468 GI_16506300-S TIGA1 5q21-q22 0.206 0.685 −3.030 GI_5902039-S RABL2B 22q13.33 0.078 0.684 −3.647 GI_31982913-S FLJ12953 2p13.1 0.313 0.682 −2.449 GI_7705579-A LCMT1 16p12.3-p12.1 0.258 0.682 −2.733 GI_14249553-S FLJ14800 12q13.13 0.332 0.681 −2.336 GI_42655683-S NTNG1 1p13.3 0.294 0.680 −2.530 GI_33188457-A UBE2D2 5q31.2 0.192 0.680 −3.046 GI_24797146-S SEPHS2 16p11.2 0.049 0.677 −3.720 GI_30410793-A PSME3 17q21 0.327 0.675 −2.310 GI_34594658-S FLJ39616 12q24.12 0.181 0.675 −3.064 GI_32401419-S SYNPR 3p14.2 0.283 0.674 −2.536 GI_21314689-S NGLY1 3p24.2 0.268 0.673 −2.605 GI_24308166-S DKFZp761H039 12q24.11 0.376 0.673 −2.029 GI_7706195-S NEUGRIN 15q26.1 0.306 0.670 −2.377 GI_21359821-S RNASE3L 5p13.3 0.358 0.669 −2.086 GI_33356141-S C9orf91 9q32 0.310 0.667 −2.334 GI_21361744-S STRBP 9q33.3 0.200 0.666 −2.886 GI_13569955-S ARPC5L 9q33.3 0.324 0.666 −2.246 GI_32307135-A NNAT 20q11.2-q12 0.191 0.665 −2.928 GI_37556084-S LOC375088 20p11.23 0.364 0.665 −2.020 GI_16306547-S SARS 1p13.3-p13.1 0.266 0.665 −2.542 GI_16950659-S CDK7 5q12.1 0.277 0.664 −2.483 GI_13128967-S MGC1136 8p12 0.348 0.663 −2.092 GI_39930484-S MCSC 9q34.11 0.201 0.662 −2.850 GI_29570797-S PPAT 4q12 0.257 0.659 −2.539 GI_8922103-S BM045 16p13.3 0.336 0.659 −2.121 GI_6006024-S MPP1 Xq28 0.316 0.658 −2.228 GI_4506330-S PTS 11q22.3-q23.3 0.335 0.657 −2.110 GI_4501912-S ADAM23 2q33 0.162 0.657 −2.997 GI_37545891-S DKFZP5640092 14q11.2 0.343 0.656 −2.065 GI_37543775-S KIAA1340 12p11.22 0.328 0.656 −2.145 GI_41222851-S DKFZP564D166 17q23.3 0.170 0.656 −2.952 GI_16445392-S CDH12 5p14-p13 0.282 0.655 −2.373 GI_23238232-S HMGN4 6p21.3 0.281 0.653 −2.365 GI_34222360-S ATP1A1 1p21 0.211 0.652 −2.717 GI_17999533-S PRPF18 10p13 0.194 0.650 −2.779 GI_24308110-S DKFZp56401863 12p11.23 0.182 0.649 −2.831 GI_31377794-S CALM1 14q24-q31 0.079 0.648 −3.332 GI_14456712-S HBQ1 16p13.3 0.276 0.647 −2.339 GI_4507128-S SNRPE 1q32 0.338 0.646 −2.004 GI_15451873-I B3GALT3 3q25 0.274 0.644 −2.323 GI_6912393-S GNG3 11p11 0.250 0.637 −2.394 GI_17999532-S PHYH 10pter-p11.2 0.305 0.635 −2.088 GI_45237192-S KIAA0446 1q22 0.184 0.635 −2.709 GI_42734431-S NLK 17q11.2 0.236 0.632 −2.429 GI_31343354-S PAQR3 4q21.21 0.321 0.631 −1.975 GI_27477044-A MT 22q13.31 0.267 0.630 −2.250 GI_32261311-S HSPC039 18q12 −0.026 0.630 −3.686 GI_37546978-S LOC376872 2p24.1 0.204 0.626 −2.537 GI_37574716-S TRAPPC5 19p13.2 0.148 0.623 −2.789 GI_4506516-S RGS2 1q31 0.187 0.622 −2.595 GI_16507966-S ENO2 12p13 0.286 0.621 −2.079 GI_42476192-S MGC8721 8p12 0.220 0.619 −2.403 GI_4503872-I GAD1 2q31 −0.005 0.619 −3.497 GI_17149845-S FKBP3 14q21.3 0.256 0.618 −2.206 GI_21314771-S ESDN 3q12.1 0.220 0.617 −2.392 GI_24308256-S KIAA1576 16q23.1 −0.012 0.616 −3.514 GI_12232478-S ARV1 1q42.2 0.280 0.614 −2.055 GI_24308180-S KIAA1354 9p22 0.287 0.613 −2.012 GI_18375679-S WBP11 12p12.3 0.265 0.612 −2.120 GI_14916518-S AP3M2 8p11.2 0.273 0.610 −2.068 GI_34850063-S NDUFC1 4q28.2-q31.1 0.110 0.603 −2.820 GI_28933464-S STX12 1p35-p34.1 0.241 0.600 −2.152 GI_19913429-S ATP5J 21q21.1 0.212 0.598 −2.280 GI_24430168-A PANK2 20p13 0.194 0.597 −2.364 GI_20127554-S HSPC111 5q35.2 0.091 0.597 −2.866 GI_42660513-S LOC390616 15q25.1 0.089 0.595 −2.867 GI_16753206-S UBQLN2 Xp11.23-p11.1 −0.005 0.593 −3.306 GI_13128995-S CUEDC2 10q24.32 0.251 0.593 −2.050 GI_4503766-S FMR2 Xq28 0.022 0.592 −3.164 GI_16933538-A GLMN 1p22.1 0.258 0.587 −1.970 GI_37539736-S LOC343990 2q11.2 0.047 0.585 −2.992 GI_21956644-S MTPN 7q33 0.227 0.585 −2.108 GI_27735126-S SLC35F3 1q42.2 0.084 0.577 −2.755 GI_7549818-A RABL2A 2q13 0.088 0.577 −2.735 GI_6806888-S HSF2 6q22.31 0.127 0.570 −2.499 GI_22035573-A 3-Sep 22q13.2 0.226 0.570 −2.006 GI_21389416-S FLJ31795 17q21.31 0.197 0.569 −2.148 GI_4758873-S TM9SF2 13q32.3 0.194 0.568 −2.154 GI_42655672-S LOC163404 1p21.3 0.227 0.567 −1.982 GI_7262387-S NARS 18q21.2-q21.3 0.197 0.567 −2.133 GI_42734423-S PSMD14 2q24.2 0.087 0.565 −2.658 GI_40255050-S FLJ12770 1q23.3 0.156 0.565 −2.321 GI_24430187-S PIGH 14q11-q24 0.114 0.565 −2.527 GI_13259542-A SLC25A14 Xq24 0.128 0.564 −2.457 GI_34850073-S CGI-150 17p13.3 0.183 0.564 −2.177 GI_41281989-I TRNT1 null 0.121 0.564 −2.485 GI_37555873-S LOC346887 8q23.1 0.184 0.564 −2.171 GI_28178835-S IDH3A 15q25.1-q25.2 0.209 0.564 −2.049 GI_6996006-A DNM1L 12p11.21 0.174 0.563 −2.220 GI_21361928-S SLC38A1 12q13.11 −0.015 0.560 −3.115 GI_4757883-S C18orf1 18p11.2 0.159 0.559 −2.266 GI_33598967-S LMO7 13q22.2 0.166 0.559 −2.232 GI_17921992-I TUBA2 13q11 0.123 0.555 −2.413 GI_22035640-S MGST3 1q23 0.210 0.554 −1.977 GI_40804463-S C20orf103 20p12 0.144 0.554 −2.305 GI_34734070-S GABRD 1p 0.175 0.554 −2.149 GI_39725933-S SERPINF1 17p13.1 0.051 0.551 −2.736 GI_37538719-S LOC377527 7q21.12 0.133 0.546 −2.303 GI_33519435-A CCNB1IP1 14q11.2 0.148 0.544 −2.214 GI_42659948-S LOC283400 12q13.13 0.186 0.541 −2.006 GI_18491027-S C15orf15 15q21 0.114 0.538 −2.343 GI_8923591-S HARC 9p24.1 0.067 0.536 −2.559 GI_4885584-S SAE1 19q13.32 0.141 0.536 −2.196 GI_24430136-S DXS9879E Xq28 0.109 0.535 −2.340 GI_7657300-S KLHDC2 14q22.1 0.010 0.529 −2.783 GI_7549792-A TBL2 7q11.23 0.055 0.528 −2.560 GI_41327765-A ALEX2 Xq21.33-q22.2 0.154 0.527 −2.072 GI_41327727-S CLTC 17q11-qter 0.058 0.527 −2.537 GI_37577121-I UBE2J1 6q15 −0.094 0.520 −3.227 GI_31543933-S VMP 6p22.2 0.134 0.518 −2.106 GI_31543390-S PEG10 7q21 0.068 0.512 −2.394 GI_32455261-A PRDX5 11q13 0.145 0.511 −2.009 GI_22749102-S FLJ36175 2q24.2 0.084 0.509 −2.291 GI_37595544-S PCTK2 12q23.1 0.055 0.509 −2.432 GI_6996009-S GARS 7p15 0.064 0.507 −2.381 GI_37549971-S KIAA1311 5q32 0.142 0.505 −1.987 GI_38327536-S INPP5A 10q26.3 −0.045 0.501 −2.865 GI_42741681-S ZNF265 1p31 0.036 0.494 −2.431 GI_42476122-S RUSC1 1q21-q22 0.101 0.489 −2.084 GI_37541920-S KIAA0789 12q23.3 −0.067 0.487 −2.883 GI_33519472-S NDFIP1 5q31.3 0.057 0.485 −2.274 GI_34147622-S RPA2 1p35 0.095 0.482 −2.069 GI_27436965-A KCNAB1 3q26.1 0.068 0.482 −2.199 GI_21389526-S MGC29761 9q34.3 −0.047 0.481 −2.750 GI_4502280-S ATP1B3 3q23 0.060 0.478 −2.212 GI_37546921-S LOC339804 2p15 0.079 0.475 −2.105 GI_37577147-A NCKIPSD 3p21 0.007 0.473 −2.437 GI_30102943-S COAS2 1q21.1 0.098 0.472 −1.992 GI_24797085-S KPNB3 13q32.2 0.062 0.469 −2.145 GI_37552180-S KIAA1246 6p21.2-p21.1 0.055 0.467 −2.168 GI_21536352-S ACTL6 7q22 0.071 0.465 −2.078 GI_22749192-S FLJ38564 Xq21.2 −0.033 0.464 −2.571 GI_27436982-S KCND2 7q31 0.021 0.460 −2.291 GI_7657674-S VAMP2 17p13.1 0.047 0.459 −2.160 GI_21071055-S SMARCA4 19p13.2 −0.020 0.453 −2.441 GI_37059763-S GPHN 14q23.3 0.058 0.447 −2.030 GI_12383063-S FNDC4 2p23.3 0.001 0.444 −2.293 GI_21361092-S TPST1 7q11.21 0.040 0.444 −2.098 GI_18765755-A DYRK1A 21q22.13 −0.061 0.443 −2.580 GI_37622352-S NME5 5q31 −0.054 0.441 −2.537 GI_31982879-S HMGB1 13q12 −0.011 0.441 −2.329 GI_34147695-S C6orf93 6q24.2 0.034 0.438 −2.094 GI_4557712-S LAMB3 1q32 0.036 0.431 −2.045 GI_4502286-S ATP2B1 12q21.3 −0.149 0.431 −2.936 GI_29648312-S LOC57168 22.q12.1 −0.002 0.423 −2.181 GI_8923321-S FLJ20344 Xp11.3 −0.037 0.423 −2.345 GI_7661957-S BTF 6q22-q23 0.021 0.423 −2.067 GI_18201904-S GPI 19q13.1 0.009 0.420 −2.111 GI_34147515-S UAP1 1q23.3 −0.043 0.418 −2.348 GI_7669496-S JWA 3p14 −0.040 0.411 −2.291 GI_21359928-S XPNPEP1 10q25.3 −0.092 0.411 −2.543 GI_23346417-S MINA 3q11.2 −0.085 0.409 −2.496 GI_13899304-S CD99L2 Xq28 −0.008 0.406 −2.112 GI_32698821-S LOC90637 7p22.3 −0.038 0.406 −2.256 GI_12669913-S E2F3 6p22 −0.150 0.403 −2.781 GI_33695108-S RAB9P40 9q33.3 −0.006 0.400 −2.065 GI_40556362-S NT5C3 7p14.3 0.010 0.396 −1.969 GI_21071045-A SMARCA1 Xq25 −0.021 0.395 −2.112 GI_16306542-A FGF13 Xq26.3 −0.090 0.394 −2.440 GI_18254455-S TSGA2 21q22.3 −0.067 0.392 −2.311 GI_7662646-S PTDSS1 8q22 −0.014 0.386 −2.023 GI_13376430-S FLJ13397 10p13 −0.020 0.385 −2.047 GI_21362099-S ELOVL4 6q14 −0.082 0.385 −2.343 GI_42476300-S TOMM70A 3q12.2 −0.135 0.383 −2.597 GI_28274685-S ZNF545 19q13.12 −0.029 0.380 −2.063 GI_22060272-S LOC221424 6p21.1 −0.022 0.379 −2.020 GI_34222114-S DKFZp566D234 4q32.3 −0.075 0.378 −2.276 GI_42476197-S MGC15407 2p16.1 −0.159 0.378 −2.680 GI_24497588-S ARX Xp21 −0.174 0.374 −2.735 GI_32307179-S CHCHD2 7p11.2 −0.062 0.372 −2.177 GI_13937360-S TRF4-2 16q12.1 −0.119 0.371 −2.447 GI_5209326-S AMD1 6q21-q22 −0.027 0.369 −1.991 GI_30089957-S MRPS36 5q13.2 −0.059 0.368 −2.140 GI_33469953-A RBM12 20q11.21 −0.051 0.367 −2.095 GI_42662641-S LOC203547 Xq28 −0.058 0.366 −2.125 GI_24308070-S DKFZP566K1924 2p14 −0.170 0.365 −2.667 GI_4502536-S CACNB4 2q22-q23 −0.228 0.364 −2.947 GI_37549396-S LOC376965 2q24.1 −0.034 0.363 −1.992 GI_4758403-S FRG1 4q35 −0.073 0.362 −2.177 GI_37546946-S LOC375211 2p13.1 −0.066 0.359 −2.126 GI_37546535-S LOC377960 Xq25 −0.047 0.351 −1.990 GI_4557656-S ICT1 17q25.1 −0.087 0.351 −2.183 GI_4505230-S MPDZ 9p24-p22 −0.073 0.348 −2.095 GI_7661579-I DKFZP434J154 7p22.1 −0.116 0.348 −2.304 GI_14042940-S eIF2A 3q25.1 −0.218 0.330 −2.711 GI_33519463-S NDUFA4 7p21.3 −0.149 0.327 −2.355 GI_4506562-S RNGTT 6q16 −0.121 0.325 −2.208 GI_14149798-S RAB6C 2q21.1 −0.105 0.320 −2.098 GI_34222118-S SYT4 18q12.3 −0.098 0.306 −1.991 GI_32307149-A OGT Xq13 −0.188 0.306 −2.433 GI_25952086-S KCNA5 12p13 −0.127 0.298 −2.092 GI_44680150-S CRI1 15q21.1-q21.2 −0.154 0.297 −2.218 GI_5729809-S EBP Xp11.23-p11.2

−0.165 0.296 −2.269 GI_41281590-S MBNL1 3q25 −0.166 0.295 −2.270 GI_33504488-S ZD52F10 19q13.12 −0.111 0.295 −2.001 GI_9257239-A SDFR1 15q22 −0.168 0.294 −2.270 GI_4758483-S GSTO1 10q25.1 −0.149 0.292 −2.172 GI_34147390-S MGC4093 19q13.2 −0.335 0.292 −3.120 GI_21265079-S MRPL18 6q25.3 −0.126 0.284 −2.014 GI_21735623-A YWHAZ 8q23.1 −0.134 0.271 −1.987 GI_21314612-S EIF2S3 Xp22.2-p22.1 −0.211 0.270 −2.360 GI_4557600-S GABRA2 4p12 −0.145 0.268 −2.024 GI_33859846-S COX7A3 4q22.3 −0.175 0.267 −2.163 GI_30061561-A GABRB3 15q11.2-q12 −0.172 0.266 −2.149 GI_19224662-S my048 Xq22.1-q22.3 −0.149 0.262 −2.012 GI_7705904-S DHRS8 4q22.1 −0.139 0.261 −1.960 GI_4757797-S APG5L 6q21 −0.222 0.260 −2.363 GI_4557580-S FABP5 8q21.13 −0.414 0.259 −3.394 GI_7669474-A ADAR 1q21.1-q21.2 −0.400 0.256 −3.294 GI_7705962-S RAB9B Xq22.1-q22.3 −0.243 0.254 −2.441 GI_15150808-S LOC90701 18q21.32 −0.172 0.247 −2.045 GI_44680134-A BDH 3q29 −0.166 0.241 −1.984 GI_34222351-S C1orf37 1q32.1 −0.170 0.235 −1.976 GI_22035617-S OSBPL8 12q14 −0.188 0.221 −1.995 GI_34147678-S HOOK1 1p32.1 −0.421 0.214 −3.203 GI_42716286-S FLJ10904 5q14.1 −0.396 0.213 −3.050 GI_21359921-S FLJ10581 17p13.3 −0.245 0.210 −2.229 GI_27436972-S KCNB1 20q13.2 −0.239 0.195 −2.125 GI_30260191-I ATPIF1 null −0.359 0.166 −2.615 GI_37059769-S MGC42105 5p12 −0.317 0.160 −2.355 GI_37541941-S LOC376142 12q21.31 −0.273 0.154 −2.093 GI_37537715-A EIF5 14q32.32 −0.329 0.153 −2.380 GI_20336240-S PCSK1N Xp11.23 −0.269 0.135 −1.980 GI_23110945-A PSMA7 20q13.33 −0.285 0.133 −2.050 GI_44955928-S KIAA1078 1q32.1 −0.362 0.120 −2.400 GI_6598326-S TSTA3 8q24.3 −0.413 0.110 −2.640 GI_31377710-S FLJ22104 11q14.2 −0.330 0.108 −2.170 GI_39725695-S L3MBTL2 22q13.31-q13.

−0.300 0.107 −2.005 GI_41349440-A SEC31L1 4q21.22 −0.394 0.086 −2.416 GI_37577165-I LIAS 4p14 −0.314 0.085 −1.972 GI_11968046-S PAF53 9p13.2 −0.376 0.051 −2.149 GI_7549807-S DNAJA2 16q12.1 −0.456 0.049 −2.600 GI_14195617-A MAP2 2q34-q35 −0.500 0.041 −2.839 GI_21314666-S CPSF3 2p25.1 −0.361 0.033 −1.977 GI_13375980-S FLJ22419 3p24.3 −0.461 0.030 −2.538 GI_27479471-S KIAA1130 14q24.1 −0.393 0.028 −2.127 GI_14150138-S PYM 12q13.2 −0.393 0.028 −2.128 GI_14861835-A ALG2 9q22.33 −0.385 0.024 −2.065 GI_29893561-S C6orf210 6q21 −0.398 0.017 −2.107 GI_32698747-S ZNF248 null −0.434 0.004 −2.257 GI_32306540-S TRIT1 1p35.3-p34.1 0.707 0.375 2.346 GI_13787188-A CYP2C8 10q23.33 0.675 0.385 1.993 GI_33354243-A NELF 9q34.3 0.569 0.160 2.331 GI_14141194-S SDF2 17q11.2 0.551 0.207 1.968 GI_34147364-S MGC4707 11p11.2 0.536 0.098 2.404 GI_21536354-A TAF6 7q22.1 0.491 0.058 2.303 GI_20127520-S C22orf5 22q12 0.474 0.004 2.460 GI_4503502-S EIF2B1 12q24.31 0.449 0.010 2.275 GI_13129121-S MGC2654 16p13.2 0.444 −0.002 2.305 GI_20336760-S HEBP1 12p13.1 0.440 −0.008 2.304 GI_4508008-S ZNF177 19p13.2 0.436 0.014 2.179 GI_21361453-S PYCR2 1q42.12 0.436 0.049 2.008 GI_39753966-S CSPG5 3p21.3 0.435 0.017 2.156 GI_41281667-S SP2 17q21.32 0.432 −0.117 2.787 GI_38569431-A B1 7p14 0.430 0.044 2.002 GI_20127496-S PPP5C 19q13.3 0.382 −0.164 2.728 GI_30023852-S MTSS1 8p22 0.380 −0.018 2.009 GI_14971416-S TRIM28 19q13.4 0.366 −0.273 3.192 GI_7706183-I ARL61P4 12q24.31 0.359 −0.330 3.452 GI_27477112-S SREBF2 22q13 0.348 −0.054 2.007 GI_16332359-A CDC2L1 1p36.33 0.340 −0.186 2.610 GI_21450690-S U2AF1L3 19q13.12 0.338 −0.315 3.256 GI_31341683-S LOC340371 8q24.3 0.329 −0.099 2.121 GI_34222318-S DULLARD 17p13 0.297 −0.315 3.042 GI_7661599-S DKFZP564B147 Xq26.3 0.294 −0.132 2.094 GI_40786546-S ANKRD11 16q24.3 0.272 −0.136 2.001 GI_4504724-S IRF3 19q13.3-q13.4 0.267 −0.153 2.057 GI_11321616-S DPYSL4 10q26 0.266 −0.204 2.306 GI_14149955-S DKFZp564A176 3q21.3 0.265 −0.138 1.972 GI_13129061-S LENG5 19q13.4 0.257 −0.183 2.154 GI_38683864-A RBBP6 16p12.2 0.248 −0.346 2.953 GI_19718752-S BAP1 3p21.31-p21.2 0.237 −0.250 2.392 GI_39811997-A AES 19p13.3 0.233 −0.297 2.612 GI_15431289-S RPL11 1p36.1-p35 0.225 −0.180 1.974 GI_8567387-S PER3 1p36.23 0.223 −0.213 2.128 GI_42660142-S LOC387908 13q12.11 0.222 −0.337 2.769 GI_14150081-S MGC4399 1p36.22 0.217 −0.238 2.226 GI_18379352-S WFDC1 16q24.3 0.214 −0.377 2.952 GI_42734336-S DKFZp434K0410 16p11.2 0.210 −0.290 2.459 GI_4502896-S CLPTM1 19q13.2-q13.3 0.210 −0.279 2.399 GI_21237780-S WASF3 13q12 0.210 −0.222 2.110 GI_32481212-S MK-STYX 7q11.23 0.208 −0.254 2.265 GI_21361675-S FEZL 3p14.2 0.204 −0.223 2.086 GI_18034689-S C20orf4 20pter-q12 0.203 −0.289 2.420 GI_41406096-S DVL3 3q27 0.188 −0.256 2.176 GI_34147334-S FLJ20811 Xq21.33-q22.3 0.181 −0.250 2.107 GI_32401444-S SPRED2 2p14 0.179 −0.384 2.819 GI_29725623-S COL23A1 5q35.3 0.169 −0.332 2.478 GI_4503664-S FBLN2 3p25.1 0.165 −0.446 3.107 GI_37552472-S LOC286088 8p23.3 0.163 −0.253 2.030 GI_38788371-S AQR 15q14 0.156 −0.268 2.075 GI_37541013-S LOC374395 11q12.3 0.154 −0.368 2.604 GI_24307876-S POR 7q11.2 0.147 −0.347 2.449 GI_34734074-A SLC22A18 11p15.5 0.142 −0.395 2.695 GI_6006015-S LGALS1 22q13.1 0.142 −0.329 2.328 GI_4826959-S QARS 3p21.3-p21.1 0.140 −0.376 2.581 GI_13376750-S FLJ11848 11q13.4 0.137 −0.378 2.573 GI_14589873-A DOM3Z 6p21.3 0.133 −0.278 2.018 GI_33943097-S RAB5B 12q13 0.132 −0.329 2.281 GI_37552345-S LOC374876 19p13.3 0.132 −0.315 2.207 GI_4758315-S ETV5 3q28 0.129 −0.295 2.090 GI_31317254-S NLGN2 17p13.1 0.120 −0.401 2.626 GI_38202225-S ZZEF1 17p13.2 0.117 −0.312 2.116 GI_16933541-I FN1 2q34 0.116 −0.350 2.316 GI_15431298-S RPL18 19q13 0.115 −0.358 2.354 GI_15208653-S DGCR6 22q11.21 0.114 −0.485 3.094 GI_4507658-S TPR 1q25 0.108 −0.396 2.536 GI_4507284-S STX10 19p13.13 0.108 −0.398 2.548 GI_29171741-A PPAP2B 1pter-p22.1 0.105 −0.376 2.405 GI_38570070-A CLDN10 13q31-q34 0.104 −0.389 2.478 GI_42661292-S LOC400586 17p11.2 0.104 −0.374 2.391 GI_15431299-S RPL18A 19p13 0.098 −0.329 2.115 GI_13569888-S DC-TM4F2 10q23.1 0.098 −0.326 2.099 GI_38372922-A BSG 19p13.3 0.094 −0.629 4.015 GI_7661883-S HELZ 17q24.2 0.094 −0.328 2.091 GI_24475893-S GNB2L1 5q35.3 0.088 −0.359 2.233 GI_18860906-S USP31 1p36.12 0.087 −0.480 2.932 GI_21314637-S NEUROD2 17q12 0.078 −0.503 3.039 GI_23097284-I 384D8-2 22q13.33 0.078 −0.363 2.206 GI_14249383-S C14orf128 14q12 0.064 −0.394 2.314 GI_22538458-A NCOA1 2p23 0.054 −0.594 3.548 GI_38045937-S RNF144 2p25.2-p25.1 0.054 −0.347 2.000 GI_31455613-S F-LANa 17p13.2 0.053 −0.388 2.223 GI_22749426-S FLJ36874 11q12.1 0.053 −0.392 2.244 GI_21359956-S FLJ21047 1q23.3 0.050 −0.365 2.083 GI_19923288-S PIK3CD 1p36.2 0.048 −0.377 2.137 GI_37547125-S D2S448 2p25 0.042 −0.387 2.168 GI_44889474-S RAB6IP1 11p15.4 0.039 −0.425 2.365 GI_34147360-S MGC2749 19p13.11 0.034 −0.416 2.292 GI_4505122-S MBP 18q23 0.023 −0.433 2.341 GI_4758083-S CSPG3 19p12 0.021 −0.620 3.592 GI_24371247-S HCBP6 Xq28 0.020 −0.372 1.976 GI_23397665-S SIN3A 15q24.2 0.012 −0.408 2.140 GI_21536450-A PHF1 6p21.3 0.005 −0.512 2.741 GI_45433544-S KIAA0460 1q21.2 0.005 −0.391 2.012 GI_30795195-S LHX2 9q33-q34.1 0.003 −0.386 1.973 GI_38570104-S RAIN 19q13.33 0.001 −0.449 2.329

indicates data missing or illegible when filed

SUPPLEMENTARY TABLE 9 This file contains the detailed results of the aSyn ratio QTL analysis, with the SNIPs found to be associated to aSynL:total ratio in unaffected cortex with a p-value < 1.0e−3.03 Frequency Genotype Mean log-ratio CHR SNP p-value G11 G12 G22 G11 G12 G22 G11 G12 G22 4 rs356168 2.70E−07 0.2409 0.4678 0.2913 C/C C/T T/T 0.219 −0.0311 −0.1256 16 rs1115023

2.55E−06 0.259 0.4601 0.281 T/T T/G G/G 0.1442 0.02985 −0.1591 23 rs5970014 5.78E−06 0.3177 0.2265 0.4558 A/A A/G G/G 0.1697 −0.03346 −0.0857 8 rs1095497

7.37E−06 0.2396 0.5014 0.2591 A/A A/G G/G 0.1533 0.01286 −0.1502 6 rs2842846 1.35E−05 0.06887 0.4325 0.4986 C/C C/A A/A 0.3844 0.03439 −0.07017 18 rs754789 1.52E−05 0.01729 0.2363 0.7464 C/C C/T T/T −0.1298 −0.1868 0.07097 3 rs7629689 1.56E−05 0.1378 0.5044 0.3578 A/A A/T T/T 0.1398 0.06685 −0.1419 12 rs1104672

2.10E−05 0.002755 0.1377 0.8595 C/C C/A A/A 0.161 0.264 −0.03542 6 rs6907063 2.91E−05 0.1437 0.4655 0.3908 A/A A/G G/G 0.3147 −0.04062 −0.06416 2 rs1257178 2.96E−05 0.1243 0.4641 0.4116 C/C C/T T/T −0.2197 −0.01866 0.1009 17 rs1476462 3.54E−05 0.03824 0.3059 0.6559 T/T T/C C/C −0.2575 −0.1116 0.08288 6 rs9384860 3.78E−05 0.06685 0.429 0.5042 C/C C/A A/A 0.3594 0.03505 −0.06963 2 rs4667454 3.81E−05 0.1191 0.4515 0.4294 C/C C/T T/T −0.1869 −0.03337 0.1089 15 rs4778757 4.40E−05 0.03581 0.27 0.6942 C/C C/G G/G −0.1789 −0.1412 0.07331 6 rs7451240 4.93E−05 0.03047 0.2992 0.6704 A/A A/G G/G −0.3104 −0.1065 0.06814 21 rs1444358 5.63E−05 0.04665 0.3265 0.6268 C/C C/T T/T −0.3686 −0.06907 0.06838 6 rs9296193 6.00E−05 0.04959 0.3554 0.595 C/C C/G G/G −0.2418 −0.08327 0.08057 4 rs7686587 6.64E−05 0.09706 0.3588 0.5441 G/G G/A A/A 0.1722 0.09876 −0.08532 6 rs9377153 6.96E−05 0.0303 0.3003 0.6694 A/A A/G G/G −0.3104 −0.1005 0.06862 10 rs4394764 6.98E−05 0.03581 0.3388 0.6253 T/T T/C C/C 0.2054 0.1213 −0.06732 6 rs6925433 7.14E−05 0.06977 0.4419 0.4884 A/A A/G G/G −0.1704 −0.0691 0.1079 11 rs1104244

7.21E−05 0.05556 0.3306 0.6139 A/A A/G G/G 0.363 0.06239 −0.05111 8 rs7013706 7.27E−05 0.169 0.4626 0.3684 A/A A/C C/C −0.1484 −0.02445 0.1182 6 rs1547334 7.59E−05 0.005935 0.1.662 0.8279 A/A A/G G/G −0.7411 −0.1738 0.04595 1 rs1203323

7.79E−05 0 0.1709 0.8291 C/C C/T T/T NA −0.2098 0.04206 21 rs9980326 7.93E−05 0.04696 0.3287 0.6243 A/A A/G G/G −0.3369 −0.0629 0.06848 13 rs2764015 8.01E−05 0 0 1191 0.8809 C/C C/A A/A NA −0.2529 0.03883 11 rs1104244

8.07E−05 0.05234 0.3333 0.6143 A/A A/G G/G 0.3743 0.05818 −0.05311 21 rs9984859 8.19E−05 0.04482 0.3305 0.6246 A/A A/T T/T −0.3686 −0.06057 0.06632 3 rs1093501

8.62E−05 0.008264 0.2397 0.7521 T/T T/C C/C 0.2497 0.1677 −0.04774 6 rs1320588

8.85E−05 0.04638 0.3333 0.6203 C/C C/G G/G 0.3959 0.07865 −0.04231 1 rs1203678

9.44E−05 0 0.1737 0.8263 C/C C/T T/T NA −0.2014 0.04723 6 rs6905873 9.50E−05 0.2051 0.486 0.309 A/A A/T T/T −0.05891 −0.07648 0.178 6 rs2065147 9.56E−05 0.01412 0.3136 0.6723 C/C C/A A/A −0.2691 −0.1151 0.07394 6 rs812479 0.000102 0.2171 0.4543 0.3286 C/C C/A A/A −0.1062 −0.04047 0.143 11 rs1089490

0.000107 0.07438 0.4904 0.4353 C/C C/G G/G 0.2659 0.04396 −0.08035 14 rs1162145

0.000108 0.0112 0.2353 0.7535 T/T T/G G/G 0.438 0.1466 −0.04678 6 rs6912415 0.00011 0.234 0.4791 0.2869 T/T T/C C/C −0.1021 −0.02471 0.1505 11 rs1229015

0.00011 0.2219 0.5216 0.2565 A/A A/C C/C 0.1041 0.05804 −0.1634 11 rs1122170

0.000111 0.008772 0.1257 0.8655 A/A A/G G/G −0.7268 −0.1698 0.04287 4 snp_a-189

0.000112 0.03274 0.2589 0.7083 G/G G/A A/A −0.3652 −0.09996 0.05433 17 rs9905834 0.000114 0.03641 0.3501 0.6134 G/G G/A A/A 0.3837 0.0811 −0.0528 6 rs9366911 0.000122 0.0854 0.4325 0.4821 C/C C/G G/G −0.2337 −0.03488 0.08587 8 rs1947299 0.000129 0.1523 0.454 0.3937 G/G G/A A/A −0.1644 −0.02246 0.1066 6 rs1115341

0.000131 0.1602 0.4724 0.3674 G/G G/A A/A −0.0651 −0.08328 0.1472 18 rs1108243

0.000134 0.03324 0.3435 0.6233 G/G G/A A/A −0.1636 −0.112 0.07553 14 rs4902348 0.00014 0.01111 0.2389 0.75 T/T T/C C/C 0.4574 0.1409 −0.04414 6 rs9400760 0.000144 0.06354 0.4254 0.511 G/G G/C C/C 0.233 0.07083 −0.07372 12 rs1106206

0.000147 0.04167 0.3361 0.6222 A/A A/G G/G −0.1549 −0.1097 0.07935 6 rs4523125 0.000147 0.1278 0.4801 0.392 A/A A/G G/G 0.1625 0.05209 −0.1013 6 rs1246940 0.0001.52 0.108 0.4602 0.4318 G/G G/A A/A −0.2095 −0.0189 0.09587 2 rs1703328

0.000156 0.01497 0.1617 0.8234 A/A A/G G/G 0.3843 0.171 −0.05067 23 rs1731946

0.000157 0.174 0.2072 0.6188 A/A A/G G/G 0.2218 −0.02051 −0.04656 21 rs992039 0.000162 0.0423 0.3746 0.5831 C/C C/T T/T 0.2686 0.1035 −0.06498 12 rs1084860

0.000162 0.04132 0.3361 0.6226 G/G G/A A/A −0.1549 −0.1072 0.07838 7 rs4948033 0.000164 0.1989 0.4779 0.3232 G/G G/C C/C 0.1478 0.02155 −0.1058 6 rs2357128 0.000171 0.1302 0.5042 0.3657 T/T T/C C/C 0.1585 0.04918 −0.1016 6 rs1707850

0.000173 0.01705 0.2926 0.6903 T/T T/C C/C −0.2011 −0.1352 0.0594 7 rs4947522 0.000176 0.211 0.4624 0.3266 A/A A/G G/G 0.1368 0.04659 −0.106 6 rs2220790 0.000177 0.2319 0.4232 0.3449 C/C C/T T/T −0.129 0.001802 0.1179 16 rs4454988 0.00018 0.1657 0.4061 0.4282 G/G G/C C/C −0.1339 −0.0366 0.1.047 12 snp_a-206

0.000191 0.005525 0.1575 0.837 G/G G/A A/A −0.6251 −0.1706 0.04345 22 rs1003846 0.000192 0.002841 0.1023 0.8949 A/A A/G G/G −0.1864 −0.2494 0.0466 4 rs1343493

0.000195 0.08033 0.4377 0.482 A/A A/G G/G 0.1605 0.07867 −0.08609 6 rs9355389 0.000199 0.005634 0.1606 0.8338 T/T T/C C/C 0.4423 0.1906 −0.03709 6 rs829813 0.000203 0.1424 0.5029 0.3547 G/G G/A A/A 0.166 0.03407 −0.1014 6 rs2452955 0.000209 0.2127 0.4586 0.3287 C/C C/T T/T −0.125 −0.00795 0.1179 16 rs8059713 0.00021 0.1983 0.4626 0.3391 T/T T/A A/A 0.1385 0.02927 −0.1076 8 rs4874138 0.000212 0.1337 0.4875 0.3788 A/A A/G G/G −0.1323 −0.03917 0.1164 16 rs9940998 0.000213 0.1333 0.4111 0.4556 T/T T/G G/G −0.1935 −0.02114 0.08012 16 rs1731222

0.000215 0.01681 0.1541 0.8291 GIG G/A A/A 0.5988 0.1263 −0.02999 20 rs1467414 0.000215 0.02521 0.2633 0.7115 T/T T/C C/C −0.2498 −0.1201 0.06196 16 rs8043932 0.000216 0.1364 0.3864 0.4773 A/A A/T T/T −0.1833 −0.02606 0.08384 6 rs7742701 0.000216 0.1961 0.4945 0.3094 T/T T/C C/C −0.05967 −0.06896 0.1653 2 rs6737952 0.00022 0 1188 0.5028 0.3785 A/A A/G G/G 0.256 0.002549 −0.06936 6 rs6568860 0.000223 0.06534 0.4119 0.5227 T/T T/C C/C 0.233 0.06564 −0.07297 18 rs8089950 0.000226 0.1025 0.4183 0.4792 T/T T/G G/G −0.08719 −0.09137 0.1069 6 rs1687799

0.000229 0.01934 0.1768 0.8039 C/C C/A A/A −0.3282 −0.1485 0.04833 10 rs1118781

0.000232 0.1924 0.481 0.3265 G/G G/A A/A −0.1287 −0.01116 0.1258 6 rs2811686 0.000232 0.06509 0.3639 0.571 G/G G/T T/T −0.1616 −0.09668 0.0821 16 rs8045969 0.000235 0.1529 0.3971 0.45 T/T T/C C/C −0.1624 −0.01524 0.09801 15 rs1243819

0.000237 0.002941 0.2618 0.7353 G/G G/A A/A −0.3194 0.1675 −0.05314 4 rs1002620

0.000241 0.1625 0.4876 0.3499 T/T T/G G/G −0.09707 −0.04915 0.1318 3 rs1051362

0.000244 0.01404 0.1826 0.8034 A/A A/G G/G 0.392 0.1589 −0.03679 10 rs1119799

0.000246 0.01201 0.08408 0.9039 C/C C/A A/A 0.5139 0.2338 −0.02604 6 rs7745469 0.000247 0.1183 0.4958 0.3859 G/G G/A A/A 0.1788 0.04608 −0.08751 13 rs2764020 0.000251 0 0.1163 0.8837 A/A A/G G/G NA −0.2375 0.03671 6 rs2637534 0.000252 0.1933 0.4986 0.3081 G/G G/A A/A −0.04636 −0.06691 0.1751 18 rs1783649

0.000252 0.01108 0.1662 0.8227 C/C C/T T/T −0.5124 −0.1449 0.04504 18 rs1187523

0.000255 0.1185 0.5069 0.3747 A/A A/G G/G −0.1356 −0.04017 0.1142 5 rs620224 0.00026 0.005797 0.1217 0.8725 T/T T/C C/C 0.06811 0.2686 −0.025 8 rs966740 0.000271 0 0.1188 0.8812 A/A A/C C/C NA −0.2315 0.03855 5 rs4921336 0.000275 0.2039 0.4573 0.3388 G/G G/A A/A 0.1138 0.04843 −0.1151 12 rs1223079

0.000278 0.04237 0.3418 0.6158 T/T T/C C/C −0.1549 −0.1087 0.07165 4 rs1250236

0.000284 0.1653 0.427 0.4077 A/A A/G G/G −0.1312 −0.03303 0.1034 10 rs7897082 0.000287 0.002793 0.1369 0.8603 A/A A/G G/G −0.9303 −0.1859 0.03722 15 rs1051921

0.000297 0.0117 0.2398 0.7485 T/T T/A A/A 0.1464 0.1637 −0.05119 16 rs1045986

0.000307 0.1298 0.4116 0.4586 G/G G/C C/C −0.1646 −0.03143 0.08898 11 rs1229431

0.000308 0.00277 0.1302 0.867 C/C C/A A/A 0.7897 0.2052 −0.02755 10 rs363309 0.00031 0.008264 0.2011 0.7906 A/A A/G G/G 0.3791 0.1613 −0.03694 7 rs7811683 0.000314 0.2201 0.4791 0.3008 T/T T/A A/A 0.1134 0.03613 −0.1233 8 rs7003443 0.000316 0.1547 0.4834 0.3619 T/T T/C C/C −0.1595 −0.01191 0.09927 1 rs292004 0.000321 0.005525 0.105 0.8895 G/G G/A A/A −1.04 −0.1604 0.03294 4 rs2306597 0.000322 0.0338 0.338 0.6282 A/A A/G G/G 0.1982 0.1072 −0.06389 12 rs1084385

0.000327 0.05785 0.3802 0.562 A/A A/T T/T 0.287 0.05775 −0.0573 15 rs1695443

0.000336 0.005935 0.1484 0.8457 G/G G/T T/T −0.511 −0.1769 0.04922 1 rs1091728

0.000351 0.03064 0.2869 0.6825 G/G G/C C/C −0.4282 −0.06178 0.05525 13 rs831208 0.000356 0.2271 0.5103 0.2625 T/T T/C C/C −0.06575 −0.0429 0.1805 13 rs7336145 0.000361 0.002762 0.1077 0.8895 T/T T/C C/C 1.221 0.2011 −0.02248 12 rs4103862 0.000362 0.1412 0.4859 0.3729 A/A A/G G/G 0.1903 0.02494 −0.07796 8 rs1827153 0.000372 0.05249 0.2928 0.6547 G/G G/A A/A −0.2116 −0.08413 0.06684 20 rs1766582

0.000373 0.00578 0.1676 0.8266 T/T T/C C/C −0.4202 −0.1514 0.05861 7 rs2214654 0.000374 0.1922 0.4791 0.3287 A/A A/C C/C 0.1381 0.02617 −0.1022 6 rs9320441 0.000376 0.2051 0.5169 0.2781 A/A A/G G/G −0.05849 −0.04612 0.1735 11 rs4572098 0.000376 0.03039 0.2238 0.7459 C/C C/T T/T 0.2609 0.1351 −0.0404 12 rs4559767 0.000382 0.2176 0.4882 0.2941 G/G G/C C/C −0.1547 0.006372 0.09822 7 rs6465471 0.000385 0.2216 0.4737 0.3047 A/A A/G G/G 0.1104 0.04165 −0.1184 12 rs1111109

0.000387 0.02632 0.2222 0.7515 C/C C/T T/T 0.4676 0.1033 −0.03032 4 rs6838244 0.000388 0.149 0.4269 0.4241 A/A A/G G/G 0.1788 0.03158 −0.07683 6 rs6925886 0.00039 0.08564 0.4641 0.4503 T/T T/C C/C 0.1776 0.06221 −0.07878 20 rs2179604 0.000397 0.00554 0.1745 0.8199 C/C C/G G/G −0.7831 −0.1383 0.04422 10 rs4244260 0.000398 0.1478 0.458 0.3942 A/A A/G G/G −0.1374 −0.03003 0.1047 12 rs2717446 0.000398 0.01117 0.2737 0.7151 C/C C/T T/T −0.667 −0.08584 0.05585 4 rs4241838 0.000401 0.09366 0.449 0.4573 G/G G/T T/T −0.05585 −0.08981 0.1135 3 snp_a-189

0.000407 0.00554 0.09972 0.8947 G/G G/C C/C 0.3893 0.2456 −0.02336 5 rs462498 0.000407 0.1662 0.5163 0.3175 C/C C/T T/T −0.1661 −0.00633 0.1009 7 rs2598044 0.000409 0.04444 0.3556 0.6 T/T T/C C/C 0.3881 0.0497 −0.04737 11 rs2658785 0.000411 0.01377 0.1433 0.843 C/C C/T T/T −0.7832 −0.08467 0.03473 6 rs457492 0.000419 0.1606 0.5183 0.3211 C/C C/T T/T −0.1616 −0.00083 0.1008 15 rs8034910 0.00042 0.1773 0.4622 0.3605 C/C C/G G/G 0.2014 −0.02409 −0.0713 6 rs942923 0.000423 0.1285 0.4804 0.3911 T/T T/C C/C 0.1414 0.05715 −0.09106 2 rs1167758

0.000429 0.05833 0.3778 0.5639 T/T T/C C/C 0.135 0.09752 −0.07427 11 rs1222245

0.00043 0.01681 0.3361 0.6471 T/T T/A A/A 0.3537 0.1073 −0.04728 6 rs7763648 0.000437 0.06 0.4286 0.5114 G/G G/C C/C 0.2424 0.06584 −0.06348 19 rs9989732 0.000438 0.08571 0.4343 0.48 T/T T/C C/C 0.2629 0.03547 −0.05898 16 rs1770505

0.000438 0 0.1474 0.8526 A/A A/G G/G NA 0.223 −0.02179 6 rs774407 0.000441 0.2312 0.468 0.3008 A/A A/G G/G 0.1213 0.01363 −0.1101 9 rs9308278 0.000442 0.07778 0.4028 0.5194 G/G G/A A/A −0.1653 −0.06164 0.08352 20 rs1232602 0.00045 0.1278 0.4389 0.4333 T/T T/C C/C −0.1464 −0.0368 0.09473 20 rs2296236 0.000451 0.02778 0.2417 0.7306 T/T T/C C/C −0.08059 −0.1505 0.06416 4 rs6534723 0.000452 0.05638 0.3294 0.6142 T/T T/A A/A −0.09423 −0.122 0.08067 8 rs966738 0.000452 0 0.1219 0.8781 G/G G/C C/C NA −0.2222 0.03536 5 rs4580760 0.000457 0.005714 0.1229 0.8714 T/T T/G G/G −0.5833 −0.1828 0.04296 12 rs2292503 0.000459 0.1598 0.4793 0.3609 C/C C/T T/T 0.1781 0.01315 −0.07871 18 rs2112058 0.000462 0.002833 0.1133 0.8839 C/C C/A A/A −0.7783 −0.2101 0.03105 6 rs2145144 0.000463 0.1208 0.4944 0.3848 T/T T/G G/G 0.1599 0.04135 −0.09306 10 rs7075577 0.000467 0.1298 0.4586 0.4116 A/A A/G G/G −0.07667 −0.07472 0.1161 13 rs9317632 0.000469 0.03693 0.2699 0.6932 G/G G/A A/A 0.3721 0.0778 −0.04073 11 rs1938736 0.000469 0.04213 0.2949 0.6629 T/T T/G G/G −0.1699 −0.1067 0.06563 10 rs3816785 0.00047 0.03591 0.3149 0.6492 C/C C/T T/T 0.1253 0.1269 −0.05939 11 rs1735575

0.000479 0.03478 0.3275 0.6377 G/G G/A A/A 0.3936 0.07446 −0.04477 5 rs2910029 0.000488 0.07345 0.3616 0.565 G/G G/C C/C −0.2436 −0.04554 0.06536 8 rs1688558

0.000489 0.008523 0.1392 0.8523 A/A A/G G/G −0.1583 −0.2151 0.04 12 rs6580890 0.000489 0.1611 0.475 0.3639 T/T T/C C/C 0.1723 0.02061 −0.07871 4 rs1712493 0.000494 0.1803 0.5437 0.2761 T/T T/C C/C −0.1342 −0.00971 0.1194 7 rs6465472 0.000499 0.2377 0.4493 0.313 T/T T/A A/A 0.1041 0.02725 −0.1215 13 rs2875248 0.000504 0.01404 0.1489 0.8371 T/T T/C C/C −0.06123 −0.2165 0.04768 17 rs572850 0.000506 0.08989 0.4551 0.4551 T/T T/C C/C −0.2073 −0.03265 0.0815 2 rs6751992 0.000511 0.2417 0.5 0.2583 A/A A/G G/G −0.1128 −0.00435 0.1231 1 rs234115 0.000515 0.2201 0.5348 0.2451 T/T T/A A/A −0.09565 −0.02005 0.1478 1 rs2748937 0.000516 0.2222 0.5278 0.25 G/G G/C C/C −0.08939 −0.02374 0.1511 8 rs6991453 0.000528 0.1111 0.5333 0.3556 T/T T/C C/C 0.1753 0.03667 −0.09067 1 rs179853 0.000531 0.2238 0.5276 0.2486 T/T T/C C/C −0.08775 −0.02425 0.1511 13 rs9567402 0.000537 0.08333 0.4306 0.4861 C/C C/T T/T 0.1697 0.0609 −0.07761 6 rs1252603

0.000539 0.01934 0.2597 0.721 T/T T/C C/C −0.2348 −0.1179 0.0566 14 rs7400989 0.000543 0.1657 0.5 0.3343 G/G G/C C/C −0.111 −0.03202 0.1179 11 rs481843 0.000544 0.01676 0.1536 0.8296 T/T T/C C/C −0.253 −0.1704 0.04511 12 rs1105017

0.000544 0 0.09917 0.9008 T/T T/C C/C NA −0.2433 0.03384 10 rs3781264 0.000547 0.08621 0.454 0.4598 G/G G/A A/A 0.1733 0.06823 −0.07425 4 rs2672477 0.000548 0.225 0.5083 0.2667 C/C C/T T/T 0.08047 0.05938 −0.1488 8 rs6990940 0.000552 0.1343 0.5045 0.3612 A/A A/T T/T 0.163 0.03853 −0.09452 4 rs3922809 0.000553 0.1763 0.4855 0.3382 A/A A/T T/T −0.1966 0.03877 0.07661 12 rs2024077 0.000557 0.09749 0.4373 0.4652 G/G G/A A/A −0.08045 −0.07761 0.1053 4 rs4865142 0.000557 0.169 0.462 0.369 G/G G/A A/A −0.1297 −0.02431 0.103 16 rs4547336 0.000558 0.2044 0.4779 0.3177 G/G G/T T/T 0.1244 0.02902 −0.1039 6 rs7749910 0.00056 0.1243 0.4972 0.3785 A/A A/G G/G 0.1625 0.03813 −0.08751 7 rs2108016 0.000577 0.02793 0.3659 0.6061 T/T T/C C/C 0.03543 −0.1174 0.08486 6 rs4945528 0.000581 0.03989 0.4359 0.5242 C/C C/G G/G 0.2495 0.07965 −0.06299 4 rs1687626

0.000583 0.02528 0.2837 0.691 A/A A/G G/G −0.236 −0.09633 0.0654 7 rs1754720

0.000589 0.1605 0.4585 0.3811 A/A A/G G/G 0.09187 0.08251 −0.1062 4 rs6850107 0.000591 0.03955 0.3418 0.6186 A/A A/G G/G −0.1798 −0.08566 0.0731 3 rs1078001

0.000594 0.08287 0.3812 0.5359 G/G G/A A/A −0.144 −0.06465 0.08329 10 rs1118783

0.000609 0.08146 0.4972 0.4213 A/A A/G G/G 0.1253 0.06594 −0.09393 18 rs4987853 0.00061 0.02755 0.3251 0.6474 G/G G/A A/A −0.2699 −0.083 0.06299 3 rs2727952 0.000616 0.06886 0.3263 0.6048 T/T T/G G/G 0.2309 0.08723 −0.05021 1 rs599839 0.00062 0.08215 0.3569 0.5609 G/G G/A A/A 0.217 0.05458 −0.05976 14 rs1782413

0.000621 0.006098 0.2226 0.7713 T/T T/C C/C 0.424 0.1589 −0.034 8 rs1747044

0.000623 0.1078 0.4581 0.4341 G/G G/A A/A −0.2657 0.01291 0.07141 10 rs1074937

0.000628 0.03039 0.3315 0.6381 T/T T/C C/C 0.1298 0.1195 −0.05797 6 rs9487172 0.000631 0.1271 0.4972 0.3757 A/A A/C C/C 0.137 0.04321 −0.09885 17 rs1470034 0.000632 0.04735 0.3565 0.5961 C/C C/G G/G −0.3551 −0.03408 0.05793 13 rs1050769

0.000636 0.04986 0.3352 0.615 G/G G/A A/A −0.2057 −0.07115 0.06954 19 rs1297558

0.000639 0.1691 0.49 0.341 C/C C/A A/A −0.113 −0.03274 0.1165 6 rs9368942 0.00064 0.08056 0.4333 0.4861 G/G G/C C/C −0.2161 −0.02747 0.07867 20 rs998934 0.000642 0.03003 0.2763 0.6937 T/T T/C C/C 0.1818 0.1317 −0.04602 2 rs6547844 0.000646 0.01114 0.1783 0.8106 T/T T/A A/A −0.02266 −0.1858 0.05107 6 rs9285409 0.000647 0.2069 0.4914 0.3017 A/A A/C C/C 0.1646 −0.00446 −0.07945 12 rs33223 0.000649 0.06077 0.3785 0.5608 G/G G/A A/A −0.2134 −0.05555 0.0712 11 rs1222538

0.000652 0.02035 0.2994 0.6802 A/A A/G G/G 0.3103 0.1149 −0.04484 12 rs2300245 0.000655 0.03683 0.3456 0.6176 T/T T/G G/G 0.1245 0.1134 −0.06489 6 rs6568591 0.000655 0.08746 0.4723 0.4402 G/G G/A A/A 0.1786 0.05377 −0.08087 10 rs1118789

0.000661 0.05 0.3972 0.5528 C/C C/G G/G 0.168 0.08801 −0.06695 6 rs1291389 0.000662 0.04545 0.2614 0.6932 T/T T/C C/C −0.2088 −0.09985 0.05898 12 rs1282436

0.000669 0.1643 0.4791 0.3565 G/G G/A A/A 0.1684 0.01357 −0.07884 10 rs1124440

0.000669 0.002755 0.1185 0.8788 G/G G/A A/A −0.8605 −0.1857 0.03497 11 rs1126359

0.00067 0.1994 0.4848 0.3158 G/G G/C C/C 0.1314 0.02355 −0.09843 1 rs7547134 0.000671 0.116 0.4807 0.4033 C/C C/G G/G 0.1175 0.06845 −0.09272 1 rs234106 0.000673 0.2295 0.5269 0.2436 C/C C/T T/T −0.09602 −0.01813 0.1423 15 rs1464150 0.000677 0.003021 0.142 0.855 G/G G/C C/C −0.61 −0.1877 0.04106 7 rs1024479

0.000677 0.2183 0.5044 0.2773 C/C C/G G/G 0.1153 0.01939 −0.1247 4 rs1912806 0.000679 0.1385 0.3989 0.4626 A/A A/G G/G −0.1924 0.004378 0.07278 13 rs2219499 0.000681 0.1569 0.479 0.3641 G/G G/A A/A 0.2256 −0.00859 −0.0508 4 rs1702175

0.000694 0.04444 0.3333 0.6222 A/A A/G G/G −0.06333 −0.1115 0.07985 11 rs6485604 0.000696 0.005525 0.1934 0.8011 T/T T/C C/C −0.1836 −0.159 0.04672 23 rs6627369 0.000699 0.3295 0.2436 0.4269 C/C C/T T/T 0.1329 −0.06575 −0.066 8 rs3104327 0.000703 0.07536 0.3304 0.5942 T/T T/C C/C −0.2523 −0.04404 0.05676 6 rs2029555 0.000705 0.2681 0.4337 0.2982 C/C C/T T/T −0.04752 −0.07574 0.172 6 rs9398341 0.000714 0.2074 0.4972 0.2955 A/A A/C C/C −0.04422 −0.06976 0.1685 7 rs2189817 0.000715 0.1798 0.4663 0.3539 A/A A/G G/G 0.1805 −0.00236 −0.07037 1 rs3766465 0.00072 0.03621 0.2535 0.7103 G/G G/A A/A −0.3885 −0.05485 0.04733 4 rs7664565 0.000722 0.07736 0.361 0.5616 A/A A/G G/G 0.1463 0.09328 −0.06652 13 rs2706411 0.000724 0.05817 0.3684 0.5734 T/T T/C C/C 0.1852 0.08378 −0.06134 9 rs7868056 0.000726 0.1601 0.427 0.4129 T/T T/C C/C 0.1632 0.02922 −0.07369 12 rs1230127

0.000726 0 0.1131 0.8869 T/T T/C C/C NA 0.2394 −0.0314 13 rs2329285 0.000728 0.02479 0.2782 0.697 A/A A/C C/C 0.4289 0.08223 −0.03896 4 rs1310978

0.000731 0.02241 0.2241 0.7535 G/G G/C C/C −0.2206 −0.1317 0.05025 12 rs1780657

0.000731 0.005731 0.1203 0.8739 G/G G/T T/T 0.5085 0.1977 −0.02333 6 rs9488153 0.000735 0.2099 0.449 0.3411 T/T T/C C/C −0.07309 −0.05302 0.1367 11 rs1079339

0.000735 0.2327 0.482 0.2853 A/A A/T T/T 0.1597 −0.0212 −0.07189 6 rs7761223 0.000737 0.157 0.4821 0.3609 C/C C/T T/T −0.04138 −0.07833 0.1403 22 rs1305362

0.000742 0.0554 0.2825 0.662 A/A A/T T/T 0.314 0.05655 −0.03938 16 rs4780416 0.000745 0.1629 0.4829 0.3543 A/A A/G G/G −0.1596 −0.00713 0.09141 8 rs776394 0.000746 0.01381 0.1823 0.8039 G/G G/A A/A −0.4552 −0.1192 0.04272 16 rs4888055 0.000746 0.1268 0.3746 0.4985 T/T T/C C/C −0.1918 −0.0259 0.07173 5 rs6893633 0.000746 0.0442 0.2928 0.663 A/A A/G G/G −0.22 −0.08584 0.0565 8 rs1373896 0.000747 0.002778 0.1806 0.8167 C/C C/T T/T −0.5627 −0.1526 0.04561 8 rs1760418

0.000749 0.005618 0.09551 0.8989 A/A A/G G/G −0.1315 −0.2555 0.03594 18 rs1050285

0.000752 0.1153 0.5043 0.3804 T/T T/G G/G −0.1402 −0.04014 0.101 5 rs6451758 0.000761 0.04132 0.3388 0.6198 A/A A/T T/T 0.2549 0.08177 −0.05144 4 rs1705028

0.000767 0.01928 0.2176 0.7631 A/A A/G G/G 0.09917 0.1672 −0.04187 6 rs199024 0.000769 0.102 0.3768 0.5212 G/G G/A A/A 0.1932 0.06011 −0.05507 2 rs1704289

0.00077 0.01108 0.1801 0.8089 A/A A/G G/G −0.02266 −0.1834 0.04723 11 rs948133 0.000775 0.2485 0.5 0.2515 A/A A/G G/G 0.1139 0.0245 −0.1217 10 rs7906986 0.000776 0.01408 0.1803 0.8056 T/T T/C C/C −0.33 −0.148 0.03712 10 rs8178980 0.000777 0 0.133 0.867 T/T T/C C/C #VALUE! −0.2003 0.03814 20 rs1773846

0.000781 0.005731 0.1347 0.8596 G/G G/C C/C −0.4689 −0.1739 0.0438 8 rs1841019 0.000782 0.1117 0.5391 0.3492 C/C C/A A/A 0.1753 0.03637 −0.08368 8 rs1050330

0.000782 0.04959 0.3196 0.6309 T/T T/C C/C −0.1877 −0.08085 0.06579 14 rs4981259 0.000782 0.2 0.5099 0.2901 G/G G/A A/A 0.1493 0.002226 −0.08736 12 rs1074353

0.000782 0.1568 0.426 0.4172 G/G G/A A/A −0.1597 −0.01702 0.08365 10 rs2601749 0.000784 0.1528 0.4639 0.3833 C/C C/T T/T −0.06595 −0.06051 0.1258 13 rs1878410 0.000785 0.1385 0.4488 0.4127 T/T T/C C/C −0.1834 −0.00264 0.07712 4 rs2119787 0.000786 0.175 0.425 0.4 G/G G/A A/A −0.1043 −0.03613 0.104 2 rs2380609 0.000787 0.1185 0.383 0.4985 T/T T/G G/G −0.239 0.008973 0.06636 6 rs2452965 0.000794 0.1637 0.4167 0.4196 A/A A/G G/G −0.1266 −0.03083 0.1006 23 rs732572 0.000794 0.04249 0.08215 0.8754 G/G G/A A/A −0.3466 −0.1023 0.03273 10 rs7099178 0.000796 0.01994 0.2934 0.6866 G/G G/C C/C 0.1735 0.1227 −0.05402 3 rs3816529 0.000809 0.005634 0.2225 0.7718 G/G G/C C/C 0.2453 0.1601 −0.02994 15 rs7169200 0.00081 0.2194 0.4986 0.2821 T/T T/C C/C −0.127 0.01505 0.1096 11 rs1089710

0.000812 0.207 0.5015 0.2915 C/C C/T T/T −0.1406 0.01057 0.1014 4 rs1540052 0.000813 0.07182 0.3508 0.5773 C/C C/T T/T −0.2118 −0.05003 0.06519 19 rs2974211 0.000817 0.1047 0.3953 0.5 G/G G/A A/A 0.1391 0.06821 −0.08017 4 rs2726686 0.000817 0.231 0.507 0.262 G/G G/A A/A 0.07072 0.06316 −0.1516 8 rs1709201

0.000818 0.008621 0.2241 0.7672 A/A A/G G/G −0.1745 0.1808 −0.04582 4 rs1399404 0.000819 0.2284 0.507 0.2646 G/G G/C C/C 0.07839 0.05154 −0.1447 1 rs6692930 0.00082 0.03047 0.2936 0.6759 C/C C/T T/T 0.2622 0.1007 −0.04659 7 rs1153163

0.000829 0.1737 0.465 0.3613 A/A A/C C/C 0.1674 0.009214 −0.07542 5 rs1051267

0.000832 0.02493 0.2909 0.6842 C/C C/A A/A 0.343 0.0948 −0.04114 10 rs1254531 0.000832 0.01393 0.234 0.7521 A/A A/G G/G 0.5048 0.1092 −0.03538 17 rs8064630 0.000833 0.0554 0.3435 0.6011 A/A A/G G/G −0.1943 −0.06592 0.06965 21 rs4591420 0.000834 0.1091 0.528 0.3628 T/T T/C C/C −0.1945 −0.00368 0.09313 6 rs1291402 0.000836 0.05292 0.2702 0.6769 C/C C/A A/A −0.1507 −0.1069 0.06325 8 rs1325582

0.000837 0.1127 0.5268 0.3606 G/G G/C C/C 0.1753 0.04075 −0.08086 5 rs1368378 0.000846 0.1425 0.4644 0.3932 C/C C/T T/T 0.1762 0.02572 −0.07179 8 rs884530 0.00085 0.01111 0.175 0.8139 T/T T/C C/C −0.4837 −0.1258 0.04277 17 rs4890120 0.000854 0.01412 0.1949 0.791 A/A A/G G/G −0.4886 −0.1111 0.03947 21 rs9306015 0.000855 0.213 0.5 0.287 T/T T/A A/A −0.1439 −0.00939 0.09452 8 rs1199174

0.000857 0.01111 0.2306 0.7583 C/C C/A A/A −0.4911 −0.1008 0.05121 11 rs4073610 0.000858 0.1954 0.4828 0.3218 A/A A/T T/T 0.1798 −0.01599 −0.06832 13 rs1050736

0.000862 0.08832 0.4387 0.4729 G/G G/A A/A −0.1919 −0.03362 0.08084 13 rs9571907 0.000872 0.1524 0.482 0.3657 G/G G/A A/A 0.2328 −0.01815 −0.04794 9 rs1076069

0.000872 0.1264 0.4425 0.431 C/C C/T T/T −0.158 −0.03299 0.08297 6 rs1115328

0.000874 0.1597 0.5266 0.3137 A/A A/C C/C −0.1472 −0.00152 0.1011 13 rs1329682 0.000881 0.1552 0.4684 0.3764 C/C C/A A/A 0.2166 −0.00503 −0.05142 13 rs9526671 0.000882 0.02228 0.2368 0.7409 G/G G/A A/A −0.2693 −0.1051 0.05565 14 rs1048404

0.000891 0.04749 0.2626 0.6899 G/G G/C C/C 0.3505 0.0576 −0.03562 2 rs1169527 0.000891 0.04709 0.2964 0.6565 A/A A/G G/G −0.2039 −0.08766 0.05547 13 rs4884976 0.000892 0.05248 0.3499 0.5977 C/C C/T T/T 0.2316 0.06443 −0.06439 16 rs1164566

0.000901 0.06887 0.3774 0.5537 T/T T/C C/C 0.2201 0.05959 −0.05651 5 rs1051266

0.000902 0.005714 0.1171 0.8771 C/C C/T T/T −0.6711 −0.1728 0.03419 1 rs1252579 0.000905 0.2095 0.5391 0.2514 G/G G/A A/A −0.1249 0.02001 0.1122 4 rs795985 0.000907 0.03878 0.3324 0.6288 T/T T/G G/G 0.385 0.04943 −0.04303 13 rs7319124 0.000913 0.06069 0.3468 0.5925 C/C C/T T/T 0.3256 0.02981 −0.05108 2 rs4408769 0.000917 0.163 0.3978 0.4392 A/A A/G G/G −0.1733 0.006445 0.07041 9 rs4842173 0.000917 0.08939 0.3855 0.5251 C/C C/T T/T −0.1539 −0.0486 0.08194 13 rs342673 0.000919 0.07182 0.3204 0.6077 A/A A/G G/G −0.2137 −0.0541 0.05856 4 rs1172373

0.00092 0.09366 0.449 0.4573 G/G G/A A/A −0.04395 −0.08712 0.1085 4 rs4861163 0.00092 0.03922 0.381 0.5798 A/A A/G G/G 0.1576 0.08954 −0.06706 10 rs1235895

0.000922 0.005587 0.1229 0.8715 C/C C/G G/G −0.3843 −0.1883 0.03832 4 rs1003258

0.000936 0.1946 0.515 0.2904 T/T T/C C/C −0.08545 −0.02474 0.1464 7 rs2722269 0.000937 0.04942 0.3634 0.5872 G/G G/A A/A 0.3199 0.04282 −0.0553 6 rs4895759 0.000939 0.01462 0.307 0.6784 T/T T/A A/A −0.1892 −0.1063 0.06716 12 rs33229 0.00094 0.06128 0.3844 0.5543 T/T T/C C/C −0.2134 −0.05398 0.06677 16 rs8059982 0.000953 0.1519 0.49 0.3582 G/G G/C C/C 0.1374 0.03751 −0.09402 8 rs2935295 0.000961 0.03047 0.3019 0.6676 C/C C/T T/T 0.1944 0.1118 −0.04856 6 rs1291401 0.000963 0.05234 0.2617 0.686 T/T T/C C/C −0.1507 −0.1063 0.06132 7 rs4947934 0.000963 0.259 0.4711 0.27 T/T T/A A/A 0.1682 −0.04941 −0.05155 10 rs1050967

0.000963 0.09915 0.4448 0.4561 C/C C/T T/T 0.1218 0.06403 −0.08596 6 rs4946854 0.000966 0.1326 0.4475 0.4199 C/C C/T T/T 0.138 0.05223 −0.08014 3 rs4973856 0.000966 0.0884 0.3646 0.547 T/T T/A A/A 0.2109 0.04895 −0.05517 10 rs7904517 0.000968 0.131 0.4226 0.4464 C/C C/T T/T −0.1225 −0.04399 0.09724 6 rs7765175 0.000976 0.1547 0.489 0.3564 T/T T/C C/C −0.05086 −0.0666 0.1345 23 rs1109436

0.000982 0.1232 0.1541 0.7227 A/A A/G G/G −0.181 −0.05225 0.05134 2 rs1092868

0.000986 0.1891 0.4957 0.3152 C/C C/G G/G 0.1318 0.007078 −0.1019 8 rs1113608

0.000986 0.006061 0.1758 0.8182 T/T T/G G/G 0.431 0.1596 −0.03907 4 rs1760079

0.000991 0.03933 0.3287 0.632 A/A A/C C/C −0.1798 −0.08865 0.06467 20 rs2143618 0.000999 0.01183 0.3077 0.6805 G/G G/A A/A 0.3223 0.1157 −0.04602

indicates data missing or illegible when filed 

1. A method to determine predisposition or risk to develop Parkinson's Disease (PD) in a subject in need thereof comprising: (a) providing a biological sample from a subject in need thereof, (b) determining a ratio of SNCA long transcript to SNCA total transcript in the subject's biological sample and (c) comparing the ratio of SNCA long transcript to SNCA total transcript from the subject sample to a reference ratio of SNCA long transcript to SNCA total transcript, wherein the reference ratio is associated with a non-PD status, and wherein an increased ratio of SNCA long transcript to SNCA total transcript in the subject's sample compared to the reference ratio of SNCA long transcript to SNCA total transcript is indicative of a risk for developing Parkinson's Disease.
 2. A method to diagnose PD in a subject in need thereof, the method comprising: (a) providing a biological sample from a subject in need thereof, (b) determining a ratio of SNCA long transcript to SNCA total transcript in the subject's sample and (c) comparing the ratio of SNCA long transcript to SNCA total transcript from the subject's sample to a ratio of SNCA long transcript to SNCA total transcript in a reference sample from healthy individuals/non-PD status, wherein an increased ratio of SNCA long transcript to SNCA total transcript in the subject's sample compared to the ratio of SNCA long transcript to SNCA total transcript in the reference non-PD status sample indicates that the subject is suffering from Parkinson's Disease.
 3. The method of claim 2, further comprising comparing the ratio of SNCA long transcript to SNCA total transcript from the subject to a reference ratio of SNCA long transcript to SNCA total transcript for a PD disease status; wherein a ratio of SNCA long transcript to SNCA total transcript in the subject's sample which is similar or comparable to the reference ratio of SNCA long transcript to SNCA total transcript for a PD status indicates that the subject is suffering from PD.
 4. A method to diagnose PD in a subject in need thereof, comprising: (a) providing a biological sample from a subject, (b) determining a ratio of SNCA long transcript to SNCA total transcript in the sample obtained from the subject; (c) comparing the ratio of SNCA long transcript to SNCA total transcript from the subject to a reference ratio of SNCA long transcript to SNCA total transcript for a PD disease status; wherein a ratio of SNCA long transcript to SNCA total transcript in the subject's sample which is similar or comparable to the reference ratio of SNCA long transcript to SNCA total transcript for a PD status indicates that the subject is suffering from PD.
 5. The method of claim 4, further comprising comparing the ratio of SNCA long transcript to SNCA total transcript from the subject's sample to a ratio of SNCA long transcript to SNCA total transcript in a reference sample from healthy individuals/non-PD status, wherein an increased ratio of SNCA long transcript to SNCA total transcript in the subject's sample compared to the ratio of SNCA long transcript to SNCA total transcript in the reference non-PD status sample indicates that the subject is suffering from Parkinson's Disease.
 6. The method of claim 3, 4 or 5, wherein the PD disease status is determined by any suitable method, including but not limited to a physical examination of the subject, a neurological examination of the subject, a brain scan, or a combination thereof.
 7. The method of claim 1 to 4, wherein the subject is not diagnosed with PD.
 8. The method of claim 1 to 4, further comprising a physical examination of the subject, a neurological examination of the subject, a brain scan, or a combination thereof.
 9. The method of any one of claims 1 to 4 further comprising a step of sequencing nucleic acids isolated from the subject's sample to determine the presence or absence of a PD-risk associated SNP, wherein the presence of a PD-risk associated SNP is further indicative that the subject is at risk of developing PD or is suffering from PD.
 10. The method of claim 9, wherein the SNP is rs356168C/C risk-associated variant, rs356165 risk-associated variant, rs2736990 risk-associated variant, any other risk associated SNP, or any combination thereof.
 11. The method of claim 1-4, wherein the subject is suspected of having PD or is at risk of developing PD based on the presence of any one of parkinsonism symptoms.
 12. The method of any one of claims 1 to 4, wherein the method is carried out in the absence or presence of dopamine affecting agent administered to the subject, wherein an increased ratio of SNCA long transcript to SNCA total transcript in the presence of dopamine compared to the ratio of SNCA long transcript to SNCA total transcript in the absence of dopamine is indicative of a subject having an increased risk to develop PD.
 13. A method to identify a candidate agent which has a therapeutic effect on PD, the method comprising: (a) providing a sample from a cortical neuron cell culture, (b) determining a ratio of SNCA long transcript to SNCA total transcript in a sample from the cortical neuron cell culture, wherein the sample is obtained in the presence and absence of a candidate agent, wherein a lowered ratio of SNCA long transcript to SNCA total transcript in the sample in the presence of the candidate agent is indicative of an agent which is a therapeutic agent for treatment of PD.
 14. A method to identify a candidate agent which has a therapeutic effect on PD, the method comprising: (a) providing a sample from an animal model of PD; (b) determining a ratio of SNCA long transcript to SNCA total transcript in the sample from an animal model of PD, wherein the sample is obtained in the presence and absence of a candidate agent, administered to the animal model of PD, wherein a lowered ratio of SNCA long transcript to SNCA total transcript in the sample in the presence of the candidate agent is indicative of an agent which is a therapeutic agent for treatment of PD.
 15. A method to determine a therapeutic effect of a candidate agent in a subject suffering from PD, the method comprising: (a) determining a ratio of SNCA long transcript to SNCA total transcript in a sample from a subject suffering from PD, wherein the sample is obtained in the presence and absence of a candidate agent, wherein a lowered ratio of SNCA long transcript to SNCA total transcript in the sample in the presence of the candidate agent is indicative of an agent which is a therapeutic agent for treatment of PD.
 16. The method of claim 13, 14 or 15, wherein the lowered ratio of SNCA long transcript to SNCA total transcript in the sample in the presence of the candidate agent is due to a reduced level of SNCA long transcript in the presence of the candidate agent compared to level of SNCA long transcript the absence of the candidate agent.
 17. The method of claim 13, 14 or 15, wherein the subject is diagnosed with PD and is not administered dopamine affecting agents.
 18. The method of claim 15, wherein the subject is diagnosed by clinical symptoms, imaging of dopamine uptake, or combination thereof.
 19. The method of any one of claims 13 to 15, wherein a ratio of SNCA long transcript to SNCA total transcript is determined by quantifying SNCA long transcript and SNCA total transcript.
 20. The method of any one of claim 1, 2, 4, 13, 14, or 15, further comprising isolating nucleic acids from the subject's biological sample.
 21. The method of any one of claim 1, 2, 4, 13, 14, or 15, further comprising quantifying the levels of SNCA long transcript and SNCA total transcript, wherein the levels of SNCA long transcript and SNCA total transcript are quantified.
 22. The method of claim 1, 2, 4, 13, 14, or 15, wherein the ratio of SNCA long transcript to SNCA total transcript is determined in a CSF sample, blood sample, plasma, or serum.
 23. A kit comprising PCR primers to carry out step (b) of the method of any one of claim 1, 2, or 4 and instructions to carry out steps (a), (b) and (c) of the method of any of claim 1, 2, or
 4. 24. A kit comprising at least one PCR primer to selectively quantify the SNCA long transcript and SNCA total transcript in a sample from a subject according to any one of claim 1, 2, or 4, so as to determine the ratio of SNCA long transcript and SNCA total transcript, and instructions to carry out steps (a) and (b) of the method of any of claim 1, 2, or
 4. 25. A method of treating PD in a subject in need thereof, the method comprising: (a) providing a biological sample from a subject in need thereof, (b) determining a ratio of SNCA long transcript to SNCA total transcript in the subject's sample, (c) comparing the ratio of SNCA long transcript to SNCA total transcript from the subject's sample to a reference ratio of SNCA long transcript to SNCA total transcript, wherein the reference ratio is associated with a non-PD status, and (d) administering a dopamine affecting agent, wherein the dopamine affecting agent is administered if there is an increased ratio of SNCA long transcript to SNCA total transcript in the subject's sample compared to the ratio of SNCA long transcript to SNCA total transcript in the reference non-PD status sample.
 26. The method of claim 25, further comprising comparing the ratio of SNCA long transcript to SNCA total transcript from the subject to a reference ratio of SNCA long transcript to SNCA total transcript, wherein the reference ratio is associated with a PD disease status; wherein the dopamine affecting agent is administered if the ratio of SNCA long transcript to SNCA total transcript in the subject's sample is similar or comparable to the reference ratio of SNCA long transcript to SNCA total transcript for a PD status.
 27. The method of claim 25, wherein the subject is not administered a dopamine affecting agent.
 28. The method of claim 25, further comprising isolating nucleic acids from the subject's biological sample.
 29. The method of claim 25, further comprising quantifying the levels of SNCA long transcript and SNCA total transcript, wherein the levels of SNCA long transcript and SNCA total transcript are quantified.
 30. The method of claim 25 or 26, wherein the dopamine affecting agent is levodopa, a dopamine agonist, a MAO-B inhibitor, a dopa decarboxylase inhibitor, a COMT inhibitor, or any combination thereof.
 31. The method of claim 30, wherein the MAO-B inhibitor is selegiline or rasagiline. 